bam file flags- interpretation

Question

[krp0001]

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

[Sukhi Singh]

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

Answer 1

[Zev.Kronenberg]

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

[Sukhi Singh]

Thats worth the effort!

[krp0001]

Thank you Zev, for your quick reply..!

Answer 2

[Simply Bioinformatics]

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

ENJOY ;)

1. https://broadinstitute.github.io/picard/explain-flags.html
2. http://www.samformat.info/sam-format-flag
3. http://www.samformat.info/sam-format-flag-single
4. https://ppotato.wordpress.com/2010/08/25/samtool-bitwise-flag-paired-reads/