bcftools variant calling query

Question

[f1978hp]

"During variant calling bcftools compares the average mapping quality of reads supporting a variant with those they don't. If there is a significant difference it will skip this variant. " Are there someone that can explain me how to create a BAM file with the reads that didn't supported the variant calling process in this case?

Answer 1

[Kevin Blighe]

Can you provide the source of the statement?

Anyway, not a direct answer but you can negate this filtering by just filtering out all reads below a certain MAPQ threshold, e.g., MAPQ 60:

samtools view -bq 60 Aligned.bam > Aligned_FiltMAPQ.bam

Then, there cannot be a statistically significant difference (based on MAPQ) between those reads that support a call versus those that don't.

Kevin

[f1978hp]

Hi Kevin!

Thanks for your interesting!

The source of the statement is another answer to my query that I was propose later. See the link Command line explain There you will undertand the problem better.