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.
bcftools variant calling query
"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?
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Kevin Blighe
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f1978hp •
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f1978hp •
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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
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