Hello,
I'm currently using samtools mpileup like this:
The output format is pileup here's a short example:
Is there any way to convert his pileup format to bed. For this short example the desired output would be:
Thanks.
I'm currently using samtools mpileup like this:
Code:
samtools mpileup -l target_regions.bed file1.bam file2.bam file3.bam > mpileup-all
Code:
chr1 6384820 N 0 * * 1 G E 0 * * 0 * * 0 * * 1 G A0 * * chr1 6384821 N 0 * * 1 G H 0 * * 0 * * 0 * * 1 G H0 * * chr1 6384822 N 0 * * 1 C I 0 * * 0 * * 0 * * 1 C G0 * * chr1 6384825 N 0 * * 1 C I 0 * * 0 * * 0 * * 1 C G0 * * chr1 6384826 N 0 * * 1 C I 0 * * 0 * * 0 * * 1 C G0 * * chr1 6384827 N 0 * * 1 C I 0 * * 0 * * 0 * * 1 C G0 * * chr1 6384828 N 0 * * 1 C I 0 * * 0 * * 0 * * 1 C G0 * *
Code:
chr1 6384820 6384822 chr1 6384825 6384828
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