where are parameters of SNPQ(snp quality) and TD(total read depth) defined when calling variants using SAMTOOLS and GATK?
This paper tells us how to filter variants using parameters SNPQ(snp quality) and TD(total read depth) ,but i can not find where these two parameters are.
I would well appreciated if you tell me the detailed file where these two lie.
Thx in advance!
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Variant callers like samtools/bcftools and GATK assign confidence score to the identified variants. They can be found in the vcf file column 6 (QUAL tag). The same vcf file also has DP field under the INFO tag. You can filter the variants from the vcf file based on these two values.
You mean SNPQ(snp quality) is QUAL and TD(total read depth) is DP?
I do not know why this article did not use term "QUAL" and "DP".
Thx!
Your interpretation is likely correct. QUAL and DP are probably what you want.