Samtools View -X Option
samtools view -X ...bam
can anyone explain the second column of the result?
such as:
FCC0TWYACXX:5:1204:20202:38832 p2 1 797438 37 100M = 796991 -447 GGTAGATAAATAGATGGATGATGGATGGATGATAGATAGCTGATAGTAGATAAGGTAGATAGTAGATAGATGATAGATGGATGGATGATAGATGATTGAT BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB^^^ONRefaXXIO^XX^YYPIP_cYXXIIbX[b^[QJKXeRKd[KJ[b^cd^ebYSQKYcP^a
like:
p2
pPR1
pPR2
puU2
purR2
pPr1
....
what do these mean?
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Pierre Lindenbaum
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siyu •
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1 answer
It's a "verbose" view of the sam flag; http://picard.sourceforge.net/explain-flags.html
I suppose 'p' stands for "read paired" (sam flag=1), etc... you should run samtools without -X to get the (standard) numeric value of the sam-flag.
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Ram
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