From 7cd40bfbc28c6138cd1a2c4dd5bd3ed87ae82724 Mon Sep 17 00:00:00 2001 From: fubar2 Date: Sat, 28 Sep 2024 18:18:32 +1000 Subject: [PATCH 1/4] update VCF information fields - completely different now --- tools/sniffles/sniffles.xml | 85 +++++++++++++++++++++---------------- 1 file changed, 48 insertions(+), 37 deletions(-) diff --git a/tools/sniffles/sniffles.xml b/tools/sniffles/sniffles.xml index 0d68dc9cd85..6c8362ab282 100644 --- a/tools/sniffles/sniffles.xml +++ b/tools/sniffles/sniffles.xml @@ -188,45 +188,56 @@ Advanced Options | Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)| +----------------------------------------+------------------------------------------------------------------------------+ - -Output -****** - -VCF Info field description - -Sniffles report multiple information in the Info field. The entries are delimited by: - -+-------------------+------------------------------------------------------------------------------------------------------+ -| IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). | -+-------------------+------------------------------------------------------------------------------------------------------+ -| CHR2= | The chromosome of the second breakpoint of the SV reported. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| END= | The position (bp) of the second breakpoint of the SV reported. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| ZMW= | For PacBio based reads, shows the number of ZMW that support the SV. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| SVTYPE= | The type of the SV. (see Alt field above) | -+-------------------+------------------------------------------------------------------------------------------------------+ -| SUPTYPE= | Indicates what evidence supports the SVs (SR: Split Reads, AL: Alignment, NR: Noisy Region). | -+-------------------+------------------------------------------------------------------------------------------------------+ -| STD_quant_start= | The standard deviation of the start breakpoints. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| STD_quant_stop= | The standard deviation of the stop breakpoints. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| RNAMES= | A comma separated list of read names that support the SV event. Controlled by -n Parameter. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| SVLEN= | Indicates the length of SVs. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| STRANDS= | Strand information at both breakpoints. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| SEQ= | If reportable shows the sequence of the indels. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| RE= | Number of reads supporting the variance. | -+-------------------+------------------------------------------------------------------------------------------------------+ -| AF= | Allele frequency (only if run with –genotype) | -+-------------------+------------------------------------------------------------------------------------------------------+ +VCF information fields from the VCF header + ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| Field | Kind | | Desc | ++=================+==============+=============+==+===============================================================================================+ +| PRECISE | Number=0 | Type=Flag | Description="Structural variation with precise breakpoints" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| IMPRECISE | Number=0 | Type=Flag | Description="Structural variation with imprecise breakpoints" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| MOSAIC | Number=0 | Type=Flag | Description="Structural variation classified as putative mosaic" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| SVLEN | Number=1 | Type=Integer | Description="Length of structural variation" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| SVTYPE | Number=1 | Type=String | Description="Type of structural variation" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| CHR2 | Number=1 | Type=String | Description="Mate chromsome for BND SVs" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| SUPPORT | Number=1 | Type=Integer| Description="Number of reads supporting the structural variation" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| SUPPORT_INLINE | Number=1 | Type=Integer| Description="Number of reads supporting an INS/DEL SV (non-split events only)" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| SUPPORT_LONG | Number=1 | Type=Integer| Description="Number of soft-clipped reads putatively supporting the long insertion SV" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| END | Number=1 | Type=Integer| Description="End position of structural variation" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| STDEV_POS | Number=1 | Type=Float | Description="Standard deviation of structural variation start position" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| STDEV_LEN | Number=1 | Type=Float | Description="Standard deviation of structural variation length" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| COVERAGE | Number=. | Type=Float | Description="Coverage near upstream start, center, end, downstream of structural variation" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| STRAND | Number=1 | Type=String | Description="Strands of supporting reads for structural variant" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| AC | Number=. | Type=Integer| Description="Allele count summed up over all samples" | ++-----------------+--------------+----------------+----------------------------------------------------------------------------------------------+ +| SUPP_VEC | Number=1 | Type=String | Description="List of read support for all samples" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| CONSENSUS_SUPP | Number=1 | Type=Integer| Description="Number of reads that support the generated insertion (INS) consensus sequence" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| RNAMES | Number=. | Type=String | Description="Names of supporting reads (if enabled with --output-rnames)" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| AF | Number=1 | Type=Float | Description="Allele Frequency" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| NM | Number=. | Type=Float | Description="Mean number of query alignment length adjusted mismatches of supporting reads" | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ +| PHASE | Number=. | Type=String | Description="Phasing information derived from supporting reads | ++-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ Source: https://github.com/fritzsedlazeck/Sniffles + ]]> From fd832604cb1c0491b7bf16c19e01f56204342879 Mon Sep 17 00:00:00 2001 From: fubar2 Date: Sat, 28 Sep 2024 23:24:17 +1000 Subject: [PATCH 2/4] add the option to turn off detect-large-ins which finds half a chromosome insertion. What does that mean in reads that were from a single subject so 2 independent haplotypes? --- tools/sniffles/sniffles.xml | 137 +++++++++++------- .../sniffles/test-data/expected_outcome3.vcf | 4 +- .../sniffles/test-data/expected_outcome4.vcf | 4 +- .../sniffles/test-data/expected_outcome5.vcf | 4 +- .../sniffles/test-data/expected_outcome6.vcf | 4 +- tools/sniffles/test-data/expected_output.vcf | 4 +- tools/sniffles/test-data/expected_output2.vcf | 4 +- 7 files changed, 93 insertions(+), 68 deletions(-) diff --git a/tools/sniffles/sniffles.xml b/tools/sniffles/sniffles.xml index 6c8362ab282..a6bf7c3a40f 100644 --- a/tools/sniffles/sniffles.xml +++ b/tools/sniffles/sniffles.xml @@ -16,8 +16,8 @@ Use a genome fasta file from the current history - +
- - - - + + + + +
- +
@@ -90,6 +95,7 @@ sniffles + @@ -130,19 +136,26 @@ Sniffles What is Sniffles? ***************** + Sniffles is a SV caller for long reads. Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data. SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations). Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication). +---- + Inputs ****** Known to work with Minimap2 bam as input +Optional reference fasta with matching contig names will allow deletions to be determined. + +---- Parameters ********** + General ------- @@ -164,6 +177,7 @@ General +---------------------------+-----------------------------------------------------------------------+ + Clustering Options ------------------ @@ -188,55 +202,66 @@ Advanced Options | Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)| +----------------------------------------+------------------------------------------------------------------------------+ + +---- + VCF information fields from the VCF header +****************************************** + ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| Field | Type | Description | ++==================+===========+===============================================================================================+ +| PRECISE | Flag | Structural variation with precise breakpoints | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| IMPRECISE | Flag | Structural variation with imprecise breakpoints | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| MOSAIC | Flag | Structural variation classified as putative mosaic | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| SVLEN | Integer | Length of structural variation | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| SVTYPE | String | Type of structural variation | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| CHR2 | String | Mate chromsome for BND SVs | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| SUPPORT | Integer| Number of reads supporting the structural variation | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| SUPPORT_INLINE | Integer| Number of reads supporting an INS/DEL SV (non-split events only) | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| SUPPORT_LONG | Integer| Number of soft-clipped reads putatively supporting the long insertion SV | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| END | Integer| End position of structural variation | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| STDEV_POS | Float | Standard deviation of structural variation start position | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| STDEV_LEN | Float | Standard deviation of structural variation length | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| COVERAGE | Float | Coverage near upstream start, center, end, downstream of structural variation | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| STRAND | String | Strands of supporting reads for structural variant | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| AC | Integer| Allele count summed up over all samples | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| SUPP_VEC | String | List of read support for all samples | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| CONSENSUS_SUP | Integer| Number of reads that support the generated insertion (INS) consensus sequence | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| RNAMES | String | Names of supporting reads (if enabled with --output-rnames) | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| AF | Float | Allele Frequency | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| NM | Float | Mean number of query alignment length adjusted mismatches of supporting reads | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ +| PHASE | String | Phasing information derived from supporting reads | ++------------------+-----------+-----------------------------------------------------------------------------------------------+ + + +---- + + +Source +****** -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| Field | Kind | | Desc | -+=================+==============+=============+==+===============================================================================================+ -| PRECISE | Number=0 | Type=Flag | Description="Structural variation with precise breakpoints" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| IMPRECISE | Number=0 | Type=Flag | Description="Structural variation with imprecise breakpoints" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| MOSAIC | Number=0 | Type=Flag | Description="Structural variation classified as putative mosaic" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| SVLEN | Number=1 | Type=Integer | Description="Length of structural variation" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| SVTYPE | Number=1 | Type=String | Description="Type of structural variation" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| CHR2 | Number=1 | Type=String | Description="Mate chromsome for BND SVs" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| SUPPORT | Number=1 | Type=Integer| Description="Number of reads supporting the structural variation" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| SUPPORT_INLINE | Number=1 | Type=Integer| Description="Number of reads supporting an INS/DEL SV (non-split events only)" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| SUPPORT_LONG | Number=1 | Type=Integer| Description="Number of soft-clipped reads putatively supporting the long insertion SV" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| END | Number=1 | Type=Integer| Description="End position of structural variation" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| STDEV_POS | Number=1 | Type=Float | Description="Standard deviation of structural variation start position" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| STDEV_LEN | Number=1 | Type=Float | Description="Standard deviation of structural variation length" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| COVERAGE | Number=. | Type=Float | Description="Coverage near upstream start, center, end, downstream of structural variation" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| STRAND | Number=1 | Type=String | Description="Strands of supporting reads for structural variant" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| AC | Number=. | Type=Integer| Description="Allele count summed up over all samples" | -+-----------------+--------------+----------------+----------------------------------------------------------------------------------------------+ -| SUPP_VEC | Number=1 | Type=String | Description="List of read support for all samples" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| CONSENSUS_SUPP | Number=1 | Type=Integer| Description="Number of reads that support the generated insertion (INS) consensus sequence" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| RNAMES | Number=. | Type=String | Description="Names of supporting reads (if enabled with --output-rnames)" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| AF | Number=1 | Type=Float | Description="Allele Frequency" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| NM | Number=. | Type=Float | Description="Mean number of query alignment length adjusted mismatches of supporting reads" | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ -| PHASE | Number=. | Type=String | Description="Phasing information derived from supporting reads | -+-----------------+--------------+----------------+-----------------------------------------------------------------------------------------------+ - -Source: https://github.com/fritzsedlazeck/Sniffles +https://github.com/fritzsedlazeck/Sniffles ]]> diff --git a/tools/sniffles/test-data/expected_outcome3.vcf b/tools/sniffles/test-data/expected_outcome3.vcf index 397a6ea9969..7e025bfc75a 100644 --- a/tools/sniffles/test-data/expected_outcome3.vcf +++ b/tools/sniffles/test-data/expected_outcome3.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.2 ##source=Sniffles2_2.4 -##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/6/outputs/dataset_e1aae210-b20c-453b-91cd-8b3e215c9cbf.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" -##fileDate="2024/09/26 18:22:15" +##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/6/outputs/dataset_85e708bb-74e2-4686-8dca-f0e9404b4e44.dat --allow-overwrite --minsupport 1 --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" +##fileDate="2024/09/28 23:19:48" ##contig= ##contig= ##contig= diff --git a/tools/sniffles/test-data/expected_outcome4.vcf b/tools/sniffles/test-data/expected_outcome4.vcf index dbd43aa661f..fd2cc1d8cc7 100644 --- a/tools/sniffles/test-data/expected_outcome4.vcf +++ b/tools/sniffles/test-data/expected_outcome4.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.2 ##source=Sniffles2_2.4 -##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/8/outputs/dataset_ffe443bd-f07b-4644-a417-8bd2aec4cfab.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5" -##fileDate="2024/09/26 18:22:53" +##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/8/outputs/dataset_76b2ed7a-d091-4613-bda7-505cd86d4277.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5" +##fileDate="2024/09/28 23:20:28" ##contig= ##contig= ##contig= diff --git a/tools/sniffles/test-data/expected_outcome5.vcf b/tools/sniffles/test-data/expected_outcome5.vcf index 2515bd3097a..cd2c7e50003 100644 --- a/tools/sniffles/test-data/expected_outcome5.vcf +++ b/tools/sniffles/test-data/expected_outcome5.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.2 ##source=Sniffles2_2.4 -##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/10/outputs/dataset_8b1d2d1f-49f4-47d9-8390-b933099f1342.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic" -##fileDate="2024/09/26 18:23:34" +##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/10/outputs/dataset_a9aaaabe-54e2-4f60-9a73-0454076bd7c5.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --mosaic" +##fileDate="2024/09/28 23:21:10" ##contig= ##contig= ##contig= diff --git a/tools/sniffles/test-data/expected_outcome6.vcf b/tools/sniffles/test-data/expected_outcome6.vcf index 00440cf40fc..f30fa668b4e 100644 --- a/tools/sniffles/test-data/expected_outcome6.vcf +++ b/tools/sniffles/test-data/expected_outcome6.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.2 ##source=Sniffles2_2.4 -##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/13/outputs/dataset_43c28376-bced-457b-9bc3-79b482047f0a.dat --allow-overwrite --reference /tmp/tmpy46o57ly/files/d/8/7/dataset_d879002d-9f55-45f7-a278-e6c9b6881fe8.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" -##fileDate="2024/09/26 18:24:13" +##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/13/outputs/dataset_93c07e69-9ce4-4394-84c8-8a51cb2e2c89.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" +##fileDate="2024/09/28 23:21:51" ##contig= ##contig= ##contig= diff --git a/tools/sniffles/test-data/expected_output.vcf b/tools/sniffles/test-data/expected_output.vcf index 5202433f18b..4248228b629 100644 --- a/tools/sniffles/test-data/expected_output.vcf +++ b/tools/sniffles/test-data/expected_output.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.2 ##source=Sniffles2_2.4 -##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/2/outputs/dataset_b3c7245e-3129-45a7-9a94-f6e837049557.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" -##fileDate="2024/09/26 18:20:57" +##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/2/outputs/dataset_c3cc0dff-254a-4e6b-837f-fa8a4db7f051.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --detect-large-ins 0 --cluster-binsize 100 --cluster-r 2.5" +##fileDate="2024/09/28 23:18:28" ##contig= ##contig= ##contig= diff --git a/tools/sniffles/test-data/expected_output2.vcf b/tools/sniffles/test-data/expected_output2.vcf index ea8f80517f7..912799f5f9d 100644 --- a/tools/sniffles/test-data/expected_output2.vcf +++ b/tools/sniffles/test-data/expected_output2.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.2 ##source=Sniffles2_2.4 -##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/4/outputs/dataset_f76d3b7c-c912-4135-91ca-b3ca11aa77f2.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" -##fileDate="2024/09/26 18:21:36" +##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/4/outputs/dataset_02006b89-2710-4fcc-9ac1-52a711eebee9.dat --allow-overwrite --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" +##fileDate="2024/09/28 23:19:08" ##contig= ##contig= ##contig= From be474d8b5436b98c0409ba25b549b14d97c44ef1 Mon Sep 17 00:00:00 2001 From: fubar2 Date: Sun, 29 Sep 2024 09:26:37 +1000 Subject: [PATCH 3/4] pfaffing about trying to get the ugly markup tables to look good. Waste of time - spaces are squished where it wants. --- tools/sniffles/sniffles.xml | 59 +++++++++++++++++++------------------ 1 file changed, 31 insertions(+), 28 deletions(-) diff --git a/tools/sniffles/sniffles.xml b/tools/sniffles/sniffles.xml index a6bf7c3a40f..3e207726f47 100644 --- a/tools/sniffles/sniffles.xml +++ b/tools/sniffles/sniffles.xml @@ -160,21 +160,22 @@ General ------- -+---------------------------+-----------------------------------------------------------------------+ -| Parameter | Description | -+===========================+=======================================================================+ -| Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto | -+---------------------------+-----------------------------------------------------------------------+ -| Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before | -| | it is ignored. Default: 7 | -+---------------------------+-----------------------------------------------------------------------+ -| Minimum SV Length | Minimum length of SV to be reported. Default: 50bp | -+---------------------------+-----------------------------------------------------------------------+ -| Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. | -| | Default: 20 | -+---------------------------+-----------------------------------------------------------------------+ -| Minimum alignment length | Reads with less length aligned will be ignored. Default 100 | -+---------------------------+-----------------------------------------------------------------------+ ++----------------------------+-------------------------------------------------------------------------+ +| Parameter | Description | ++============================+=========================================================================+ +| Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto | ++----------------------------+-------------------------------------------------------------------------+ +| Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before | +| | it is ignored. Default: 7 | ++----------------------------+-------------------------------------------------------------------------+ +| Minimum SV Length | Minimum length of SV to be reported. Default: 50bp | ++----------------------------+-------------------------------------------------------------------------+ +| Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. | +| | Default: 20 | ++----------------------------+-------------------------------------------------------------------------+ +| Minimum alignment length | Reads with less length aligned will be ignored. Default 100 | ++----------------------------+-------------------------------------------------------------------------+ + @@ -182,25 +183,27 @@ Clustering Options ------------------ -+----------------------------------------+-----------------------------------------------------------------------+ -| Parameter | Description | -+========================================+=======================================================================+ -| Cluster bin size | Initial cluster bin size. Default 100 | -+----------------------------------------+-----------------------------------------------------------------------+ -| Cluster Multiplier | Multiplier for SV start position standard deviation criterion in | -| | cluster merging [2.5] | -+----------------------------------------+-----------------------------------------------------------------------+ ++---------------------+------------------------------------------------------------------------+ +| Parameter | Description | ++=====================+========================================================================+ +| Cluster bin size | Initial cluster bin size. Default 100 | ++---------------------+------------------------------------------------------------------------+ +| Cluster Multiplier | Multiplier for SV start position standard deviation criterion in | +| | cluster merging [2.5] | ++---------------------+------------------------------------------------------------------------+ + + Advanced Options ---------------- -+----------------------------------------+------------------------------------------------------------------------------+ -| Parameter | Description | -+========================================+==============================================================================+ -| Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)| -+----------------------------------------+------------------------------------------------------------------------------+ ++-------------+--------------------------------------------------------------------------------+ +| Parameter | Description | ++=============+================================================================================+ +| Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)| ++-------------+--------------------------------------------------------------------------------+ ---- From e9dbc13316af7fc2b7e5affc88a365e5642b8d95 Mon Sep 17 00:00:00 2001 From: fubar2 Date: Sun, 29 Sep 2024 17:52:12 +1000 Subject: [PATCH 4/4] bump version. I must remember to bump the version. --- tools/sniffles/sniffles.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/sniffles/sniffles.xml b/tools/sniffles/sniffles.xml index 3e207726f47..ba538bca70e 100644 --- a/tools/sniffles/sniffles.xml +++ b/tools/sniffles/sniffles.xml @@ -1,4 +1,4 @@ - + Structural variation caller using third generation sequencing 2.4