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Old 02-07-2013, 04:46 AM   #1
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Join Date: Aug 2011
Posts: 106
Default RG and header info Help

Hi I was given a file without any header or RG info. The first 2 lines of the SAM file look like this:

IAI4I:01195:00410 0 1 918230 250 17M * 0 0 GTGCATGCCTGGTGCCA 468==<41)1332*1 AS:i:170 Z0:i:170 Z1:i:170 NM:i:0
IAI4I:01009:02440 0 1 1346275 250 188M * 0 0 GAGCAGCTCAGAATGGGCCAGCTTGAAAAATGCCATCTTGGCCGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCGGATCACCTGAGGTTAGGAGTTCAAGACCACCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAAACAAAAAATTAACTAGGTGTGGTG @@DDBB?A@@55-244+4,47???CEECC3CCC?B=<=+4)2+11(1121;9;455767BB>BB?>9455*4455>>>5>>*44+37?+3+223+2=:@?@@@77656:?:?@=786:??277>756@:65+4-4+31115111;(111&111111221=???;*112222&2*2+1222+211:6;; AS:i:1880 Z0:i:1889 Z1:i:1889 NM:i:0

There is no header and RG info the file and am having trouble figuring out how to add everything back in. I know that you could use samtools or picard, but I am not sure what exactly to pass. I should also mention that this data was produced on the ion Torrent.

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