Hi, I am running Pindel on with the -M option set to 30. According to Pindel documentation:
-M/--minimum_support_for_event Pindel only calls events which have this number or more supporting reads (default 3)
It was my understanding that a variant call would need at least 30 supporting reads for that call and would therefore also have a read depth of atleast 30. however, my resulting vcfs contain many calls that have a depth much lower than 30. For example this excerpt from a call on a multiple sample (3 samples) run:
GT:AD .:0 1/.:10 1/.:24
None of these have a depth >= 30... Does anyone have an explanation for this?
Thank you
•
written
by
Dalia •
1 answer
Your example has 34 total reads covering that position. Much of the impetus for multisample calling is the ability to use information from multiple samples in making calls.
Log in to answer this question.
-
Filter variants supported by 20% of total reads
written by Ks-seq •
-
Genotyping with samtools/bcftools
written by SOHAIL
-
Pindel lower the mutation rate in indel calling
written by jinxinhao1988
-
filter vcf file heterozygous calls by allelic depth
written by molly.dunn •
-
Allelic Depth 1000 Genomes call set
written by QVINTVS_FABIVS_MAXIMVS
-
Exporting TUMOR/NORMAL VCF from Scalpel
written by Manuel
-
Pindel Reports Deletions in various ways
written by mohesan •
-
Increase percentage of reads needed to call a SNP in Unified Genotyper
written by behrimg •
-
Running Pindel On Multiple Samples Produces More Calls Per Sample Than Running Pindel On Single Sam…
written by Dalia •
-
Why Does Samtools/Bcftools Give Incorrect Genotypes And Innacurate Quality Scores?
written by Casbon •
