Originally posted by k2bhide
View Post
-
Samtools mpileup vcf format question
Hello,
I have Samtools mpileup output files in VCF format. I would like to know briefly about some of the output filelds.
How are the field values for PL:GT:GQ and PV4 calculated and what is the inference of these fields in SNPs and INDELS finding.
Following are the example lines from VCF file.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_4s_5s.bam
1 49820 . T C 54.5 . DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,2;MQ=60 PL:GT:GQ 87,12,0:1/1:72
1 49826 . G C 63.5 . DP=8;AF1=0.5;CI95=0.5,0.5;DP4=2,2,3,1;MQ=60;PV4=1, 0.0015,1,1 PL:GT:GQ 66,0,102:0/1:69
It would be really helpful if anybody would give brief explanation about how these field values are obtained.
Ketaki
-
This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...03-03-2025, 01:39 PM -
The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...02-24-2025, 06:31 AM
Leave a comment: