So here is another issue also: I am dealing with the trios and when I am
aligning the fastq files through bwa the samtools flagstat output is as
follows:
*Paternal*
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)
*Maternal*
136130484 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
132584921 + 0 mapped (97.40%:-nan%)
136130484 + 0 paired in sequencing
68065242 + 0 read1
68065242 + 0 read2
131664377 + 0 properly paired (96.72%:-nan%)
131879298 + 0 with itself and mate mapped
705623 + 0 singletons (0.52%:-nan%)
120838 + 0 with mate mapped to a different chr
76211 + 0 with mate mapped to a different chr (mapQ>=5)
*Affected:*
138757912 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
128380879 + 0 mapped (92.52%:-nan%)
138757912 + 0 paired in sequencing
69378956 + 0 read1
69378956 + 0 read2
127354738 + 0 properly paired (91.78%:-nan%)
127605104 + 0 with itself and mate mapped
775775 + 0 singletons (0.56%:-nan%)
121626 + 0 with mate mapped to a different chr
88886 + 0 with mate mapped to a different chr (mapQ>=5)
Please suggest is there any discrepancy.
Thanks
Anshika
On Thu, Jan 15, 2015 at 10:13 AM, Anshika Srivastava <anshi...@umich.edu>
wrote:
> 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
>
>
>
--
Anshika Srivastava, Ph.D
Postdoctoral Fellow
University of Michigan Medical School
Department of Human Genetics
3703 Medical Sciences II
1137 Catherine St. SPC 5618
Ann Arbor, MI 48109-5618
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