Hi there,
I'm trying to merge an output bam file of SHRiMP and an output bam file of bowtie using samtools merge but there is a problem because @SN is not identical between the two files, i tried to use -h to override the header but it didn't work.
Anyone knows how to work around this problem without adjusting the files manually?
In case anyone needed them, here are the files headers:
file1:
@HD VN:1.0 SO:coordinate
@SQ SN:Chr17 LN:75158596
@PG ID:gmapper VN:2.2.3 CL:/var/www/tavaxy/engines/galaxy/tool-data/SHRiMP_2_2_3/bin/gmapper-cs /var/www/tavaxy/files/inputFiles/0337d77e79d8d1268b8d728e3696adb1/step1/run1_lane1.csfasta.folder/fileContents.csfasta /var/www/tavaxy/files/inputFiles/0337d77e79d8d1268b8d728e3696adb1/bowtie_mapper/Chr17.fa.folder/fileContents.fa -N 4 -o 5 -h 80X
file2:
@HD VN:1.3 SO:coordinate
@SQ SN:1_2_193 LN:75
@SQ SN:1_2_252 LN:75
@SQ SN:1_2_1015 LN:75
@SQ SN:1_2_1113 LN:75
Command:
samtools merge -h header.tmp sample3.bam sample1.bam sample2.bam
[bam_merge_core] different target sequence name: '1_2_193' != 'Chr17' in file 'sample2.bam'
Thanks in advance,
Shazly
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written
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Hatem Elshazly •
These files aren't mergable with samtools or picard or any other tool that I know of. What you can do is write file 2's header to a file and then edit it to contain Chr17. You can then use process substitution to merge them into a single file:
cat header <(samtools view file1) <(samtools view file2) | samtools view -Sbo merged.bam -
Edit: Apparently using MERGE_SEQUENCE_DICTIONARIES=true in MergeSamFiles from Picard tools allows this (I just tested and confirmed this).
even with picard ? there is an option inMergeSamFiles called "MERGE_DICT" . (not tested)
Guess I've never tested that option. I'll give it a whirl.
It does in fact work (I've updated my answer). Nice to know.
Ok, I tried using Picard with the MERGE_SEQUENCE_DICTIONARIES=true option and it worked.
Thank you very much for replying.
•
written
by
Hatem Elshazly •
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