difference between read depth (DP) at site (INFO) and sample(FORMAT) level
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7.1 years ago
Ana ▴ 200

I am a bit confused between read deapth at the site level and sample level. What is the difference between these two? This is a little part of my vcf file, So I have DP at INFO and FORMAT ! This is my Site annotation

AN=662;AO=323;CIGAR=1X;DP=225

and this is my sample level annotation

GT:DP:DPR:RO:QR:AO:QA:GL    .   0/0:8:8,0:8:273:0:0:0,-2.40824,-19

I would appreciate if anyone can elp me to undersatnd the difference between these two DP. If I want to do some vcf filtering based on sample DP which cut-off threshold is recommended? Thanks to take time and respond me in advance.

read depth vcf • 3.4k views
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Entering edit mode
7.1 years ago

DP at sample level is for individual samples. At site level in INFO, it should be approximately sum of all sample level DPs

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