Variant filtering parameters

Excuse me:

After calling variants, there were some variants with high coverage but VQSRTrancheSNP99.00 to 99.90. Should these variants be accepted?

Any thing that would help me understand the issue would be much appreciated!

alignment next-gen-sequencing sequence

• 1,821 views • link

updated 4.4 years ago by Ram

• written 11.6 years ago by 897598644

1 answer

Take a look here.

Kevin

• 1 views • link

updated 4.4 years ago by Ram

• written 7.7 years ago by Kevin Blighe

More posts like this

How many base pairs are there in All exon V4+UTR from Agilent manufacture?
written 10.9 years ago by 897598644

Excuse me: I was wondering how many base pairs there are in All exon V4+UTR from Agilent manufacture. Any thing that would help me understand …
VariantRecalibrator in GATK
written 11.3 years ago by 897598644

Excuse me: I used unifiedGenotyper in GATK to call variants and filterd variants with VQSR. There were errors: ``` java -jar GenomeAnalysisTK.jar \ -T ApplyRecalibration …
bam files discordant with GATK
written 11.3 years ago by 897598644

Excuse me: After calling variants with GATK, the result showed 0/1. But when I confirmed the variants using bam files with samtools, it showed . …
Term of throughput in next generation sequencing
written 11.6 years ago by 897598644

Excuse me: How shou'd I understand the concept of throughput? Does it mean the length of read or the output data amount or the speed …
1000 Genome Project and ESP for indel or frameshift
written 11.6 years ago by 897598644

Excuse me: After calling variants of indel and frameshift, I wanted to annotate them using 1000 Genome Project and ESP.Could I get the frequency of …
gene function in refgene when using annovar
written 11.6 years ago by 897598644

Excuse me: My NGS data is whole exome sequencing data. After calling variants, I annotated variants with refGene using annovar. In the column `Func.refGene`, there …
Dot mark in 1000 genome project
written 11.6 years ago by 897598644

Excuse me: When I annotated the variants using annovar with 1000genome project. Some of the results were marked with dot mark. Did these signs mean …
how many bases in the number of inter-individual difference on average ?
written 11.7 years ago by 897598644

Excuse me I want to know how many bases there are in the number of inter-individual differences for the whole genome or whole exome. Any …
base quality in the result of mpileup
written 11.7 years ago by 897598644

Excuse me: When I analyzed the reads of variants, I used command of samtools mpileup and it printed out six colums. In the last column, …
How to find structural variants
written 11.8 years ago by 897598644

Excuse me: By far, I have found snp and indel variants in my whole exome sequencing. I want to know how to find structural variants …