Bedtools intersect drops bam header line in latest version

[jfreimer]

I am trying to use bedtools intersect and it drops the sorted status in the bam file header in bedtools 2.29.1, but not in 2.29.0

bedtools intersect -v -abam test1.bam -b test.bed -wa > test2.bam

2.29.0
@HD VN:1.0 SO:coordinate @SQ SN:chr1 LN:248956422 @SQ SN:chr2 LN:242193529 @SQ SN:chr3 LN:198295559

2.29.1
@SQ SN:chr1 LN:248956422 @SQ SN:chr2 LN:242193529 @SQ SN:chr3 LN:198295559 @SQ SN:chr4 LN:190214555

[38]

Hi, could you please share the file to repo this?

[dinvlad]

We're experiencing exactly the same issue! In our case, it's

bedtools pairtobed -abam stdin -b hg19.bed < in.bam > out.bam

This command drops any and all @PG and @RG headers from in.bam...

[arq5x]

Hi @38,

The following will reproduce the problem:

wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwRepliSeq/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam
samtools sort wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam -o wgEncodeUwRepliSeqBg02esG1bAlnRep1.sorted.bam

Note the sorted file with have the sorted indicator in the first line of the header with samtools view -H wgEncodeUwRepliSeqBg02esG1bAlnRep1.sorted.bam | less

Intersect that sorted file with a bed file, the header will lose the sorted indicator.

cat test.bed
chr1	10000000	20000000

bedtools intersect -a wgEncodeUwRepliSeqBg02esG1bAlnRep1.sorted.bam -b test.bed > wgEncodeUwRepliSeqBg02esG1bAlnRep1.sorted.intersecting.bam

[38]

Hi @arq5x , Just add a fix to this issue

[arq5x]

Thanks so much for catching this. Now fixed in master thanks to @38