Hi,
I am working on the exome data and for this I used bwa aln (option -q 15)
for aligning the fastq files. When I got the bam file I was interested in
looking for the integrity of my bam file so I did the samtools flagstat and
this is what I got:
136130484 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
118895955 + 0 mapped (87.34%:-nan%)
136130484 + 0 paired in sequencing
68065242 + 0 read1
68065242 + 0 read2
115439248 + 0 properly paired (84.80%:-nan%)
115957815 + 0 with itself and mate mapped
2938140 + 0 singletons (2.16%:-nan%)
248720 + 0 with mate mapped to a different chr
166532 + 0 with mate mapped to a different chr (mapQ>=5)
Whether this metrics looks good for the downstream exome analysis or I
should go back and do the alignment again with different options.
Thanks
Anshika
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