User: pacome.pr

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Posts by pacome.pr

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Comment: C: Sorting .bam file by tag
... I managed to make it work in the end `-k1,1g -k4.4,1n -k5,1n` must be `-k1,1 -k4.4,4g -k5,5n`. I don't know why I had to remove the "g" in front of -k1,1 to make this work. The chromosomes are not sorted numerically but this is not really important in my case. ...
written 7 months ago by pacome.pr0
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Comment: C: Sorting .bam file by tag
... Thanks for the answer, Would you be able to sort by tag 'XB' but then also by chromosome and position ? I tried : samtools view -h input.bam |\ awk -F '\t' 'NR==1 {printf("\t@HD\t%s\tSO:unsorted\n",$2);next} /^@/ {printf("\t%s\n",$0);next;} {v="";for(i=12;i<=NR;++i) {split($i,a,/[\:] ...
written 7 months ago by pacome.pr0

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