Tom, thank you for you answer. You understood my question and phrased it much better.
The individual .bam files already have @RG tags with LB: and SM: values. I switched from version 0.1.18 of samtools to version 1.0 and that solved my problem. Thanks, Tommy On 09/11/2014 20:18, "Thomas W. Blackwell" <tbla...@umich.edu> wrote: > >Unless I'm completely mistaken, I think the question is "How do I >correctly merge .bam files which already have @RG tags in them, and >their @RG ID values are all the same, even though the files are for >different individuals ?" > >If that's the question, then absolutely vanilla samtools merge is what >you want, without -h, -r or -c. The paragraph in the samtools manpage >which begins "Unless the -c or -p flags are specified ..." says that >even though the original ID values are identical, they will have distinct >suffixes in the merged .bam file. The resulting ID values may be ugly, >but they will successfully distinguish individuals. If the individual >.bam files do not already have @RG tags, then -r is what you want, >followed by a 'samtools reheader' step to fill in LB: and SM: values >in the header with the appropriate information. > > - tom blackwell - > >On Sat, 8 Nov 2014, Tommy Carstensen wrote: > >> How do I merge bam files with identical @RG IDs? How do I create a >>merged >> output with a unique @RG ID for each unique @RG SM? >> >> The manual reads: >> -r Attach an RG tag to each alignment. The tag value is inferred from >>file >> names. >> >> I have tried adding the -r option: >> samtools merge -r -R 1:100000-100200 samtools.merge.bam $bamFiles >> >> The manual reads: >> -h FILEUse the lines of FILE as Œ@¹ headers to be copied to out.bam, >> replacing any header lines that would otherwise be copied from in1.bam. >> (FILE is actually in SAM format, though any alignment records it may >> contain are ignored.) >> >> >> I have tried adding -h RG.txt: >> >> samtools merge -r -R 1:100000-100200 -h RG.txt samtools.merge.bam >>$bamFiles >> >> But I am not sure, what the contents of RG.txt should be. The example >> "Attach the RG tag while merging sorted alignments" is not clear to me. >> >> Others seem to have had the same problem: >> https://www.biostars.org/p/80150/ >> >> http://seqanswers.com/forums/showthread.php?t=33260 >> >> http://sourceforge.net/p/samtools/mailman/message/30655641/ >> >> >> Currently my RG.txt file looks like this (tab separated fields): >> grep "#1[^0-9]" RG.txt | head | rev | cut -c3- | rev >> @RG ID:1#1 PL:ILLUMINA LB:7721122 SM:EGAN000011605 >> @RG ID:1#1.1 PL:ILLUMINA LB:7721122 SM:EGAN000011605 >> @RG ID:1#1.2 PL:ILLUMINA LB:7721122 SM:EGAN000011605 >> @RG ID:1#1 PL:ILLUMINA LB:7672393 SM:EGAN000011612 >> @RG ID:1#1.1 PL:ILLUMINA LB:7672393 SM:EGAN000011612 >> @RG ID:1#1.2 PL:ILLUMINA LB:7672393 SM:EGAN000011612 >> @RG ID:1#1 PL:ILLUMINA LB:7790252 SM:EGAN000011617 >> @RG ID:1#1.1 PL:ILLUMINA LB:7790252 SM:EGAN000011617 >> @RG ID:1#1.2 PL:ILLUMINA LB:7790252 SM:EGAN000011617 >> @RG ID:1#1 PL:ILLUMINA LB:7672199 SM:EGAN000011621 >> >> >> Thanks for any help on this. >> >> Tommy >> >> >> >> -- >> The Wellcome Trust Sanger Institute is operated by Genome Research >> Limited, a charity registered in England with number 1021457 and a >> company registered in England with number 2742969, whose registered >> office is 215 Euston Road, London, NW1 2BE. >> >> >>------------------------------------------------------------------------- >>----- >> _______________________________________________ >> Samtools-help mailing list >> Samtools-help@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/samtools-help ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
