where are parameters of SNPQ(snp quality) and TD(total read depth) defined when calling variants using SAMTOOLS and GATK?

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10.2 years ago

897598644 ▴ 100

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!

next-gen sequencing alignment • 2.4k views

ADD COMMENT • link updated 3.7 years ago by Ram 44k • written 10.2 years ago by 897598644 ▴ 100

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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.

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.2 years ago by Ashutosh Pandey 12k

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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!

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.2 years ago by 897598644 ▴ 100

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Your interpretation is likely correct. QUAL and DP are probably what you want.

ADD REPLY • link updated 3.7 years ago by Ram 44k • written 10.2 years ago by Sean Davis 27k

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