Question: bcftools variant calling query
gravatar for f1978hp
12 days ago by
f1978hp20 wrote:

"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?

ADD COMMENTlink modified 7 days ago by Kevin Blighe46k • written 12 days ago by f1978hp20
gravatar for Kevin Blighe
7 days ago by
Kevin Blighe46k
Kevin Blighe46k wrote:

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.


ADD COMMENTlink written 7 days ago by Kevin Blighe46k

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.

ADD REPLYlink written 1 day ago by f1978hp20
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