Variant calling and alignment stats
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Entering edit mode
11 months ago

Hi. I am using samtools flagstats to see the statistics of my alignment file. It looks something like this: I have 10x genomics reads.

 575130408 + 0 in total (QC-passed reads + QC-failed reads)
36759786 + 0 secondary
0 + 0 supplementary
114890896 + 0 duplicates
553257360 + 0 mapped (96.20% : N/A)
538370622 + 0 paired in sequencing
269185311 + 0 read1
269185311 + 0 read2
365701236 + 0 properly paired (67.93% : N/A)
505922543 + 0 with itself and mate mapped
10575031 + 0 singletons (1.96% : N/A)
82619792 + 0 with mate mapped to a different chr
67685268 + 0 with mate mapped to a different chr (mapQ>=5)


And using picard tool after alignment to remove duplicates and getting these statistics.

            446442591 + 0 in total (QC-passed reads + QC-failed reads)
36759786 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
424569543 + 0 mapped (95.10% : N/A)
409682805 + 0 paired in sequencing
205395057 + 0 read1
204287748 + 0 read2
275640808 + 0 properly paired (67.28% : N/A)
384153847 + 0 with itself and mate mapped
3655910 + 0 singletons (0.89% : N/A)
64548392 + 0 with mate mapped to a different ch
53575771 + 0 with mate mapped to a different chr (mapQ>=5)
`

My question is why the number of properly paired reads, and other types drops? Second question is for variant calling is it mandatory to use only properly paired reads? In my case its ~67% which does not seems to be a good percentage.

Best Nadia

alignment SNP • 241 views
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