Question

bam file flags- interpretation

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10.4 years ago

krp0001 ▴ 40

Dear Users,

Recently I have aligned my Illumina reads to my reference genome. I have gone through sam file specifications but, it is quiet difficult to understand.

It would be great help if some one could explain the bam flags below.

A few lines of my aligned bam file:

HISEQ:115:C49JYACXX:4:1114:10901:17520  163     scaffold1       1       7       4M2I94M =       208     307     GCACAGAACTTTTTATTGAACAATTGGGCTACTAAATATGCTTACCAAACTCTATGGTAGTGTAGTCACAGTCTCTTAGTAGTAGTATCGATATATTGTA    CC@FFFFFFHHHHJJJJIJJJIJJJIJJJGJIJIIJIJIIIJIJJGIJIIHIIJJJJFHIGHGBHCGIJIJIJJJGIJJCEHHHHHHFFFFDDDEFEEEE    AS:i:-21        XS:i:0  XN:i:0  XM:i:2  XO:i:1  XG:i:2  NM:i:4  MD:Z:0A2G94     YS:i:-11        YT:Z:CP

Thank you

Assembly • 9.1k views

ADD COMMENT • link updated 2.9 years ago by Ram 45k • written 10.4 years ago by krp0001 ▴ 40

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Flags are explained here: How To Filter Mapped Reads With Samtools

ADD REPLY • link updated 2.9 years ago by Ram 45k • written 10.4 years ago by Sukhi Singh 11k

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8.0 years ago

Simply Bioinformatics ▴ 200

Four Main reference Sites that You might need during your adventure:

ENJOY ;)

ADD COMMENT • link updated 2.9 years ago by Ram 45k • written 8.0 years ago by Simply Bioinformatics ▴ 200

Ram · Accepted Answer · 2015-06-15

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10.4 years ago

Zev.Kronenberg 12k

There is a neat app to explain the SAM flags: http://broadinstitute.github.io/picard/explain-flags.html

ADD COMMENT • link updated 6.0 years ago by Ram 45k • written 10.4 years ago by Zev.Kronenberg 12k

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Thats worth the effort!

ADD REPLY • link 10.4 years ago by Sukhi Singh 11k

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Thank you Zev, for your quick reply..!

ADD REPLY • link 10.4 years ago by krp0001 ▴ 40