Dear All Sorry for bothering. I am doing variant calling using BCFtools mpileup then call and I would like to add a filteration step in the command for mpileup in BCF tool, but really confused about which threshold to be used for a min mapping quality. In my BAM file produced from STAR, most reads have 255 value in the MAPQ field. Now I am confused which number is correct for counting the n of unique mapped reads in STAR alignment BAM file ? I have done this by two ways, which ends up in different results:
- The number/% of unique mapped reads that one can get from the log.files output from STAR aligner
The number that I obtain when running (Most of my BAM file have the 255 value in the MAPQ filed (column 5)
samtools view -q 255 -c filteredfile.bam
So which one of these is the more accurate description of the unique mapped reads ? so that I can use 255 in the filter
so shall I set this to 255 ...
i am using the below command for mpileup in BCF tool
bcftools mpileup -Ou -o Variant/L10A2.bcf -f Ref/GCF_000002315.5_GRCg6a_genomic.fna L10A2_sortedbycordinate_fix_marked.bam -Q 20