Change Notation Of Chromosome In Bam File

Question

[hellbio]

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?

[petervangalen]

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.

Answer 1

[Zev.Kronenberg]

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.

Answer 2

[ff.cc.cc]

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