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Old 07-28-2009, 07:57 AM   #1
ptong7
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Default SAM file flag problem

Hi all,
Is any body know what's the the flag means in the SAM file.
The Flag I got looks different with the SAM manual.

Thanks!

Here is a sample of my sam file.

HWI-EAS283:8:1:1:695#0 69 * 0 0 * * 0 0 NACAAGGCATTGTTGTTGCTATCATTGCTTGCAAGCAGGAATNGCTAATGGAAGACTTCTTTTTTTTTGTGTACTT %/:56465,577-91-265//:######################################################
HWI-EAS283:8:1:1:695#0 133 * 0 0 * * 0 0 AAANCGCTACGTAATGATTGCAGTGAGCACAGAGCGCCCTACTGCACTCCAGCCTGGGAAACAGAGCGCGATTCCG ############################################################################
HWI-EAS283:8:1:1:749#0 99 chr7 91549950 37 76M = 91550245 354 NACCTATCTTAATTACGTTTCAAAGTATATACTCTTTTATAANAAATGAGCTCCATAACTTAAAAGCTAGATAACA %0:<;;9::7779<;;99979707999;::9:;::9:<<75.%*5789197978599################### XT:A:U NM:i:3 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:0T41C31A1
HWI-EAS283:8:1:1:749#0 147 chr7 91550245 37 17S59M = 91549950 -354 ATTGTGTTAGACCGTGAGTCCATAAAAATATATAGAGGTAATCTGTGGGCGTTTAGTAAATGGTGGTCCTACNACT #####################################################################B6>%42B XT:A:M NM:i:12 SM:i:37 AM:i:37 XM:i:12 XO:i:0 XG:i:0 MD:Z:2A4C9T1T4A5A6C0T0G5T1T0T6T3
HWI-EAS283:8:1:1:1047#0 69 * 0 0 * * 0 0 NTTTTTTGTTCCTTTTTTTTCAAGAGGCCAGAGGCAGAGGCCNTTGTCATTTTCTGTGTGTCCAGGTAATTGCGTA %1:::98789:::999:::::985226#################################################
HWI-EAS283:8:1:1:1047#0 133 * 0 0 * * 0 0 ACCNCGCCTGCCGAGTTTTTCCTTTCTATATTCTTAGTCGTTAAGAATGTTCTATCATGTTGTAATTTTTGTAGTC 0###########################################################################
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Old 07-28-2009, 09:30 AM   #2
nilshomer
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Quote:
Originally Posted by ptong7 View Post
Hi all,
Is any body know what's the the flag means in the SAM file.
The Flag I got looks different with the SAM manual.

Thanks!

Here is a sample of my sam file.

HWI-EAS283:8:1:1:695#0 69 * 0 0 * * 0 0 NACAAGGCATTGTTGTTGCTATCATTGCTTGCAAGCAGGAATNGCTAATGGAAGACTTCTTTTTTTTTGTGTACTT %/:56465,577-91-265//:######################################################
HWI-EAS283:8:1:1:695#0 133 * 0 0 * * 0 0 AAANCGCTACGTAATGATTGCAGTGAGCACAGAGCGCCCTACTGCACTCCAGCCTGGGAAACAGAGCGCGATTCCG ############################################################################
HWI-EAS283:8:1:1:749#0 99 chr7 91549950 37 76M = 91550245 354 NACCTATCTTAATTACGTTTCAAAGTATATACTCTTTTATAANAAATGAGCTCCATAACTTAAAAGCTAGATAACA %0:<;;9::7779<;;99979707999;::9:;::9:<<75.%*5789197978599################### XT:A:U NM:i:3 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:0T41C31A1
HWI-EAS283:8:1:1:749#0 147 chr7 91550245 37 17S59M = 91549950 -354 ATTGTGTTAGACCGTGAGTCCATAAAAATATATAGAGGTAATCTGTGGGCGTTTAGTAAATGGTGGTCCTACNACT #####################################################################B6>%42B XT:A:M NM:i:12 SM:i:37 AM:i:37 XM:i:12 XO:i:0 XG:i:0 MD:Z:2A4C9T1T4A5A6C0T0G5T1T0T6T3
HWI-EAS283:8:1:1:1047#0 69 * 0 0 * * 0 0 NTTTTTTGTTCCTTTTTTTTCAAGAGGCCAGAGGCAGAGGCCNTTGTCATTTTCTGTGTGTCCAGGTAATTGCGTA %1:::98789:::999:::::985226#################################################
HWI-EAS283:8:1:1:1047#0 133 * 0 0 * * 0 0 ACCNCGCCTGCCGAGTTTTTCCTTTCTATATTCTTAGTCGTTAAGAATGTTCTATCATGTTGTAATTTTTGTAGTC 0###########################################################################
Typically, the flag field is converted to an integer value for display. You will have to infer the bits set by their sum. In the newest trunk code, you can use "samtools view" with either the "-x" or "-X" for better viewing (C code only).
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Old 07-28-2009, 09:52 AM   #3
ptong7
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Hi nilshomer,
I try "samtools view -x aln.sorted.bam <region>".
but I got this "view: illegal option -- x"
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Old 07-28-2009, 10:03 AM   #4
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Did you download the latest developers version from the trunk (not the release)?
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Old 07-30-2009, 04:32 AM   #5
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Thanks nilshomer, It works...
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