Samtools View -X Option

Question

[siyu]

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?

Answer 1

[Pierre Lindenbaum]

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.