Hi all,
I have a bam file with chromosomal notation 1,2.... and i need it to be as chr1,chr2.....
For this i have tried, samtools view -H sample.bam > header.sam
Then edited the header.sam file with required chromosomal notation and tried samtools reheader header.sam sample.bam > out.bam
when in tried to view out.bam using samtools it says "Segemntation fault".
I also tried with PICARD, java -Xmx4g -jar ReplaceSamHeader.jar INPUT=sample.bam HEADER=header.sam OUTPUT=out.bam CREATE_INDEX=TRUE
It reports the same error with samtools i.e. segmenation fault.
Could anyone help me to fix this?
2 answers
The reads need to have the same @SQ tags for the seqid.
samtools view your.bam | perl -lane 'if($_ =~ /\@/){print $_}else{$F[2] = "chr$F[2]" if $F[2] !~ /\*/; print join "\t", @F}' | bgzip or gzip
Of coure you will need to edit your header so the @SQ tags are correct.
It changes:
3 RNAME String *|[!-()+-<>-~][!-~]* Reference sequence NAME l
like you wanted.
yes if you pipe the output to the correct compression software. I'm pretty sure you want bgzip.
I tried using the following command: samtools view my.bam | perl -lane 'if($_ =~ /\@/){print $_}else{$F[2] = "chr$F[2]" if $F[2] !~ /*/; print join "\t", @F}' | gzip - > out.bam.
The out.bam is viewed using samtools. This time it shows an error:
[bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "out.bam".
Okay. Simplest solution don't compress it. This will be a SAM file. use samtools to convert it to a BAM.
Hi, I had the same task with my chomosome notation. Bam Header Edit helped me.
About the crash, beware of samtools version. Someone experimented crashes before version 0.1.19
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This question has been answered elsewhere: Bam File: Change Chromosome Notation (see my script there). I think segmentation fault means your computer ran out of memory.