Question: samtools index error
0
gravatar for pt.taklifi
9 days ago by
pt.taklifi60
pt.taklifi60 wrote:

Hello everyone I am trying to extract uniquely aligned reads and sort them with samtools with the following command

samtools view -h -f 2 -q 10 -bS -@ 20 hg38.sam | samtools sort -n -@ 1 > hg38.sort.bam

after this when I try to index the output file

samtools index hg38.sort.bam

I get this error message

[E::hts_idx_push] Unsorted positions on sequence #16: 73874275 followed by 73874203
[E::sam_index] Read 'SRR10984462.26' with ref_name='chr16', ref_length=90338345, flags=163, pos=73874203 cannot be indexed
samtools index: failed to create index for "hg38.sort.bam": No such file or directory

any suggestions ?

alignment • 84 views
ADD COMMENTlink modified 9 days ago by Pierre Lindenbaum134k • written 9 days ago by pt.taklifi60
2
gravatar for Pierre Lindenbaum
9 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

option -n of samtools sort is for sorting on read name, not on coordinate. Remove this this.option.

ADD COMMENTlink written 9 days ago by Pierre Lindenbaum134k
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