Question: Same pipeline for exome seq variant calling with different results
0
gravatar for paumarc
5 months ago by
paumarc10
Barcelona (ICO)
paumarc10 wrote:

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.

gatk snp fastp bwa-mem • 224 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by paumarc10
3

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 REPLYlink written 5 months ago by WouterDeCoster38k
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