Perhaps this is a quoting issue. I would try putting single quotes around
the -f format string in the cammand line, rather than double quotes.
- tom blackwell -
On Thu, 26 Mar 2015, ying chen wrote:
> Hi,
>
> I am trying to use samtools split command to split my bam file into small bam
> files by read group. The input bam files are the CCLE RNASeq bams.
> It worked when I did
>
> samtools split -u G20486.Calu-1.2_noRG.bam -f "%*_%#.bam" -v
> G20486.Calu-1.2.bam
> It generated bam files with suchs as G20486.Calu-1.2_0.bam,
> G20486.Calu-1.2_1.bam, ...
> Then I tried to add RG id into resulting bam file names by
> samtools split -u G20486.Calu-1.2_noRG.bam -f "%*_%!_%#.bam" -v
> G20486.Calu-1.2.bam
> and I got the error message:
> bash: !_%#.bam: event not found
> It seems that samtools split has trouble identifying RG ID. I tried and could
> not find much info or documentation regarding samtools split except the
> samtools help split.
> Here are the bam file itself:
> samtools view G20486.Calu-1.2.bam | more
> C0UNPACXX120727:2:1207:1813:5925 419 1 11615 1 101M
> = 11780 266 TAGGAATG
> CCTGTTTCTCCACAAAGTGTTTACTTTTGGATTTTTGCCAGTCTAACAGGTGAAGCCCTGGAGATTCTTATTAGTGATTTGGGCTGGGGCCTG
> <@@DFFFDDDFHBHII
> G4I@?FCEHHFFBGEEHI@HDGCD@GFFG@GEGGBHHIBFHDIICHHG>@GHIDD7=A)?EHHFF:@>CFCCCE6?ABD<=/;5?
> CC:Z:15 PG:Z:tophat.D
> RG:Z:C0UNP.2 NH:i:3 HI:i:0 NM:i:0 CP:i:102519455 MQ:i:1 UQ:i:0
> C0UNPACXX120727:5:2214:18693:14398 163 1 11615 1 101M
> = 11780 266 TAGGAATG
> CCTGTTTCTCAACAAAGTGTTTACTTTTGGATTTTTGCCAGTCTAACAGGTGAAGCCCTGGAGATTCTTATTAGTGATTTGGGCTGGGGCCTG
> ?@@DD>DAAF4AAEFH
> EF,<<CF;FAFAC?HCC<CGHA*:CDH>DCHFHHEDBH?8DH8CFIJIIG;6;(@E>EFEE>=@BC;@>>A##############
> CC:Z:15 PG:Z:tophat.8 RG:Z:C0UNP.5 NH:i:3 HI:i:0 NM:i:1
> CP:i:102519455 MQ:i:1 UQ:i:11
>
Any help would be greatly appreciated!
>
>
Best regards,
>
> Sean
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