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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