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Friday, April 11, 2014

rehead a bam file

I downloaded some ChIP-seq bam files from the UCSC genome browser

and I found some bam files headers  are without chrY information

samtools view -H  my.sorted.bam
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10 LN:135534747
@SQ SN:chr11 LN:135006516
@SQ SN:chr12 LN:133851895
@SQ SN:chr13 LN:115169878
@SQ SN:chr14 LN:107349540
@SQ SN:chr15 LN:102531392
@SQ SN:chr16 LN:90354753
@SQ SN:chr17 LN:81195210
@SQ SN:chr18 LN:78077248
@SQ SN:chr19 LN:59128983
@SQ SN:chr20 LN:63025520
@SQ SN:chr21 LN:48129895
@SQ SN:chr22 LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrM LN:16571

for some downstream analysis, I have to rehead this bam file:

samtools view -H my.bam | sed '24 a @SQ SN:chrY LN:59373566' | samtools reheader  -  my.bam > my.reheaded.bam

sed to append a line "@SQ SN:chrY LN:59373566" at  the 24th line
ctr+v+tab to insert a tab in the terminal.

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