Need help understanding VCF specification to filter VCF file
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 15/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- documentation
Research direction
Start with the bcftools command and sample VCF record in the issue, then consult the VCF specification and relevant bcftools filtering documentation. Done means documenting how the shown FORMAT and values should be interpreted and how GQ and DP filtering applies, including the comma-separated values.
Written by the indexing model from the issue text.
Description
This is the command that I used for SNP calling
bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ov -o SNP_calling.vcf
This is an example of the output
Chr1 271 . G GAAATAGCATA,GCATA 999 . INDEL;IDV=3;IMF=1;DP=470;VDB=0.443312;SGB=-75.6152;MQSB=0.00212381;MQ0F=0;ICB=0.0308101;HOB=0.108465;AC=61,21;AN=286;DP4=311,70,89,0
;MQ=32 GT:PL 0/0:0,48,255,48,255,255 0/1:15,0,8,21,11,27 1/2:60,13,21,39,0,46 0/0:0,48,255,48,255,255 0/0:0,54,255,54,255,255 0/0:0,51,255,51,255,255 0/0:0,27,241,27,241,241
How can I filter on GQ, genotype quality and DP, read depth for each position ?
Could you please help me reading this result "0/0:0,27,241,27,241,241" ?
Genotype 0/0 : and then ? because it is different from the format GT:GQ:DP:HQ or GT:GQ:DP:AD:PL and the separator is not ":" but ","
I would be very grateful if you can help me.
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