Biostar76892

Motivation

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.

Example

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