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Biostar76892
Pierre Lindenbaum edited this page Nov 5, 2013
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3 revisions
Fix strand of two paired reads close but on the same strand http://www.biostars.org/p/76892/
##Compilation
See also Compilation.
ant biostar76892
##Options
Option | Description |
---|---|
ONLYSAVEFIXED=Boolean | only save pairs of reads fixed. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} |
DISTANCE=Integer | distance beween two reads. Default value: 500. This option can be set to 'null' to clear the default value. |
IN=File | BAM file to process. Required. |
OUT=File | BAM file fixed. Required. |
Before fixing:
samtools view src.bam | grep "HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906"
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906 177 3 1264832 37 101M = 1264940 109 AGGTGGTGAAGCATGAGATGTAGGGAGAGCTGCTTTAAAACCCAGCACAAGGCTGGTTGTACTGGCTCACACCTGTAATCCCAGGTCTTTGGGAGGCTGAG """#""""#"""#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""#""""""#""##"""""""#"#" X0:i:1 X1:i:0 BD:Z:ABBACCABBABAAABABAABAACBBABAA@AAABAABBAABB@AAAAAAABA@ABAA@BAA@@BAAAAAAAA@@BAAAABA@ABAAABAACBBACBAABAA MD:Z:0C0C0C1C0C0G1G0T1T0T0G0C0C0T0T0C0T0G0T0A0C0A2T2C0A0T0G0C1T0G0T0G2G0T0T0T0G1G0T1T1C0C0A0A0G0T0G0C0G0A1T0G1G0C0T1T0T2C0G0T0G0T0G1C1C0A1G1G0T1C0C1T0T2C0A0 RG:Z:idp63088 XG:i:0 BI:Z:ABBAEDCCCBCBBABABAAAA@CBBAB@A@@A@AAAAAAABA@@AAA@A@BA@@BAA@A@@@@BAA@A@@@A@@AAAAABA@@BAAABBACBBACBBABAA AM:i:37 NM:i:75 SM:i:37 XM:i:1 XO:i:0 MQ:i:37 XT:A:U
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906 113 3 1264940 37 101M = 1264832 -109 GGTATCTCCATGCTCGAAGCCCTGACCTACTGTATTGCCCCGAAAGTCTTCCCTGCTGTGGCTGCATCTTTTCCACGTGGATAATCTTGGTTCATCTCTAG """##"""""""""""""""""""""""""#"""""""""""""""""""""""""""#"""""""""""""""#""""""""""""#""#""##"#"##" X0:i:1 X1:i:0 BD:Z:BBAABBBBAAABBBCBAABCBA@BAAAAAAABAAAAACCCBABAAAAAAACBAAAAABABA@AA@AAABBAAAAACB@BBAAAAAAAABBBAABBBBAAAA MD:Z:0T0T1G0C0A1G0T1C0C0A1G0T0G0C0A0T0G0T0G0T0G2A0T4G0C0A0A0T0G0T0G0C1G0G0T0G1C0A0G0T0T0G0C0A4C1A0T0G0C0G0T0G2G0G1C0G0T0G0A1C0G0T0G1G0C2T2T0C0G0T0G0T0A0T1 RG:Z:idp63088 XG:i:0 BI:Z:BABADDCCBBBCBBCBAABCBA@AABAAA@AAAAA@BBBBBAAA@AA@AABA@@A@@A@BA@@A@AA@AAAAAAABB@BAAAAAAAA@CBAAABBBBAAAA AM:i:37 NM:i:74 SM:i:37 XM:i:0 XO:i:0 MQ:i:37 XT:A:U
Fixing:
java -jar dist/biostar76892.jar ONLYSAVEFIXED=true \
IN=src.bam \
OUT=fix.bam \
VALIDATION_STRINGENCY=LENIENT
result
samtools view fix.bam | grep "HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906"
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906 163 3 1264832 37 101M = 1264940 109 AGGTGGTGAAGCATGAGATGTAGGGAGAGCTGCTTTAAAACCCAGCACAAGGCTGGTTGTACTGGCTCACACCTGTAATCCCAGGTCTTTGGGAGGCTGAG """#""""#"""#"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""#""""""#""##"""""""#"#" X0:i:1 X1:i:0 BD:Z:ABBACCABBABAAABABAABAACBBABAA@AAABAABBAABB@AAAAAAABA@ABAA@BAA@@BAAAAAAAA@@BAAAABA@ABAAABAACBBACBAABAA MD:Z:0C0C0C1C0C0G1G0T1T0T0G0C0C0T0T0C0T0G0T0A0C0A2T2C0A0T0G0C1T0G0T0G2G0T0T0T0G1G0T1T1C0C0A0A0G0T0G0C0G0A1T0G1G0C0T1T0T2C0G0T0G0T0G1C1C0A1G1G0T1C0C1T0T2C0A0 RG:Z:idp63088 XG:i:0 BI:Z:ABBAEDCCCBCBBABABAAAA@CBBAB@A@@A@AAAAAAABA@@AAA@A@BA@@BAA@A@@@@BAA@A@@@A@@AAAAABA@@BAAABBACBBACBBABAA AM:i:37 NM:i:75 SM:i:37 XM:i:1 XO:i:0 MQ:i:37 XT:A:U rv:i:1
HWI-1KL149:6:C0KTCACXX:5:2107:2283:35906 83 3 1264940 37 101M = 1264832 -109 GGTATCTCCATGCTCGAAGCCCTGACCTACTGTATTGCCCCGAAAGTCTTCCCTGCTGTGGCTGCATCTTTTCCACGTGGATAATCTTGGTTCATCTCTAG """##"""""""""""""""""""""""""#"""""""""""""""""""""""""""#"""""""""""""""#""""""""""""#""#""##"#"##" X0:i:1 X1:i:0 BD:Z:BBAABBBBAAABBBCBAABCBA@BAAAAAAABAAAAACCCBABAAAAAAACBAAAAABABA@AA@AAABBAAAAACB@BBAAAAAAAABBBAABBBBAAAA MD:Z:0T0T1G0C0A1G0T1C0C0A1G0T0G0C0A0T0G0T0G0T0G2A0T4G0C0A0A0T0G0T0G0C1G0G0T0G1C0A0G0T0T0G0C0A4C1A0T0G0C0G0T0G2G0G1C0G0T0G0A1C0G0T0G1G0C2T2T0C0G0T0G0T0A0T1 RG:Z:idp63088 XG:i:0 BI:Z:BABADDCCBBBCBBCBAABCBA@AABAAA@AAAAA@BBBBBAAA@AA@AABA@@A@@A@BA@@A@AA@AAAAAAABB@BAAAAAAAA@CBAAABBBBAAAA AM:i:37 NM:i:74 SM:i:37 XM:i:0 XO:i:0 MQ:i:37 XT:A:U rv:i:1