Same pipeline for exome seq variant calling with different results
0
0
Entering edit mode
3.0 years ago
paumarc ▴ 20

Hello

we have been running a pipeline using fastp, bwa-mem, and gatk with hard filtering to perform snp calling on exome seq data. Although the coverage statistics for fastq files is similar, we obtain a huge difference in the number of reads per snp. We wonder if it could be caused by hard filtering. Otherwise, could you suggest any idea of what can be going on?

Thanks in advanced.

snp bwa-mem gatk fastp • 1.1k views
ADD COMMENT
3
Entering edit mode

Although the coverage statistics for fastq files is similar, we obtain a huge difference in the number of reads per snp.

I think that adding a bit more details here would increase your chance of getting an answer.

ADD REPLY

Login before adding your answer.

Traffic: 2213 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6