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tgen / phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
MIT License
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Filter to Targets #45

Closed PedalheadPHX closed 5 years ago

PedalheadPHX commented 5 years ago

For exomes we need to filter calls to the callable space based on our callable files (targets+/-100bp padding plus extended to end of touched exons)

### Require preprocessing
# compressed and indexed bed file 
# CAN NOT include the header lines
# contigs need to match reference
# intervals need to be intersected as overlapping independent intervals will result in the same variant being extracted multiple times
bgzip test.bed
tabix test.bed.gz

### Example call
bcftools filter \
--regions-file test.bed.gz \
--output-type z \
--output f2t.vcf.gz \
NMTRC_0002_1_PB_Whole_C1_KHSTX.bwa.hc.vcf.gz
ryanrichholt commented 5 years ago

For constitutional/germline variant calls as well as somatic?

PedalheadPHX commented 5 years ago

For any exome regardless of source

On Wed, Mar 20, 2019 at 10:16 AM Ryan Richholt notifications@github.com wrote:

For constitutional/germline variant calls as well as somatic?

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ryanrichholt commented 5 years ago

Fixed here, fd6e0b641ec4cf7abffdec0e6e4eea68105a6c38. I created extended bed files for most of the commercial Agilent kits, and also Strexome v5 and v6 here 69be1175a5d7076e55a35487abc95882fc9cc5a5