Hi,
I am working on genomics data and for this I used *bwa mem* for aligning
the fastq files.
After, I am calling SNP with samtools/bcftools but I have a question
about samtools.
Is it necessary to use a filter ("samtools mpileup -q 1" ?) on the
minimum mapping quality (MAPQ) ?
What is the best way to remove reads that map to multiple locations?
What cutoff value do you use about MAPQ?
I think it is only necessary to remove zeros but I don't find a
consensus or recommendations for good practice...
thank you !!
Emeric
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