BWA BAM

[duhuipeng]

dear author

/bwa mem -t 80 MotherHap.fa R1.fastq.gz R2.fastq.gz |samtools view -@ 70 -Sb > F0-73.bam samtools sort -@ 60 F0-73.bam -o F0-73.sort.bam samtools index F0-73.sort.bam

Then I went to check this bam file and I found a lot of mapq for 0, but it only appeared 1 time, why is that? I don't really understand. If I understand it normally, shouldn't a mapq of 0 indicate that the ID is out of line in multiple places? for example This ID appears only on chromosome 18 and only once, but mapq is 0。The other one has the same ID because it is double-ended reverse complementary

I hope to get your answer, I do not quite understand Best HuipengDu

[duhuipeng]

I mainly want to see some comparisons in the centromere， so it mapq for 0 but again only once, I am very confused that What parameters do you think I need to add to show all the comparisons in that region?

[hunglin59638]

try to use -a or -h

[pinbo]

Check the "XA:Z" tag in your bam file for each read, which gives all alternative mapping locations.