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This repository holds the docker+dockstore configuration to allow processing of WXS (Whole eXome Seqeuencing) data.
- SNV Calling
- Indel Calling
- Annotation
The process requires a set of reference files bundled with standard naming conventions. All information about the species and build can only be included in the name of the archive, the base folder name of the archive and any included README files. The archive is unpacked with the base folder name stripped so it's name has no affect on configuration of the tool.
The Human GRCh37d5 set can be found here.
The core reference bundle (core_ref_GRCh37d5.tar.gz) includes the following:
core_ref_GRCh37d5/
core_ref_GRCh37d5/genome.fa.fai
core_ref_GRCh37d5/genome.fa.dict
core_ref_GRCh37d5/genome.fa
Details on how to generate fai and dict files can be found in the samtools documentation (samtools dict, samtools faidx).
The SNV/InDel bundle (SNV_INDEL_ref_GRCh37d5-fragment.tar.gz) contains the following:
SNV_INDEL_ref/
SNV_INDEL_ref/pindel/
SNV_INDEL_ref/pindel/softRules.lst
SNV_INDEL_ref/pindel/pindel_np.gff3.gz
SNV_INDEL_ref/pindel/WXS_Rules.lst
SNV_INDEL_ref/pindel/HiDepth.bed.gz
SNV_INDEL_ref/pindel/simpleRepeats.bed.gz
SNV_INDEL_ref/pindel/pindel_np.gff3.gz.tbi
SNV_INDEL_ref/pindel/WGS_Rules.lst
SNV_INDEL_ref/pindel/HiDepth.bed.gz.tbi
SNV_INDEL_ref/pindel/simpleRepeats.bed.gz.tbi
SNV_INDEL_ref/caveman/
SNV_INDEL_ref/caveman/unmatchedNormal.bed.gz
SNV_INDEL_ref/caveman/flagging/
SNV_INDEL_ref/caveman/flagging/simple_repeats.bed.gz
SNV_INDEL_ref/caveman/flagging/centromeric_repeats.bed.gz.tbi
SNV_INDEL_ref/caveman/flagging/snps.bed.gz
SNV_INDEL_ref/caveman/flagging/simple_repeats.bed.gz.tbi
SNV_INDEL_ref/caveman/flagging/hi_seq_depth.bed.gz
SNV_INDEL_ref/caveman/flagging/centromeric_repeats.bed.gz
SNV_INDEL_ref/caveman/flagging/snps.bed.gz.tbi
SNV_INDEL_ref/caveman/flagging/hi_seq_depth.bed.gz.tbi
SNV_INDEL_ref/caveman/flagging/flag.to.vcf.convert.ini
SNV_INDEL_ref/caveman/flagging/flag.vcf.config.ini
SNV_INDEL_ref/caveman/unmatchedNormal.bed.gz.tbi
SNV_INDEL_ref/caveman/flag.vcf.config.WGS.ini
SNV_INDEL_ref/caveman/HiDepth.tsv
SNV_INDEL_ref/caveman/flag.vcf.config.WXS.ini
Details on how to generate these files can be found in the cgpCaVEManWrapper wiki and cgpPindel wiki or the protocols linked from them.