Closed deb0612 closed 3 years ago
You may need to sort your bam again after running fade out
. However if using samtools sort
doesn't work, you may have something else wrong with your bam file. I need to update our documentation. If using fade out
with the -c flag, you should run samtools sort
before fade out
and after.
@deb0612 Please let us know if this has fixed your problem -- currently, annotate
and out
with -c
flag commands may "un-sort" your sorted input for reasons of parallelism/speed. We will add warnings in the future.
It is not clear from your comment if you mean using sort AFTER the FADE commands also leads to the same indexing error?
Dear jblachly, Unfortunately, the problem is still unsolved. Whatever I sort my bam file before or after fade out.
@deb0612 We would certainly like to help solve this issue. Could you provide a minimal reproducible example? For example, could you provide SAM line that causes the error when using samtools index?
Dear @charlesgregory,
Thanks for your reply.
Here is the bam file for tesing
command I used:
$sudo docker run -v pwd
:/data blachlylab/fade annotate -b /data/test.bam /data/Homo_sapiens_assembly38.fasta > test.anno.bam
$samtools sort -n test.anno.bam >test.anno.sort.bam
$sudo docker run -v pwd
:/data blachlylab/fade out -b -c /data/test.anno.sort.bam > test.anno.sort.filtered.bam
$samtools sort -n test.anno.sort.filtered.bam >test.anno.sort.filtered.sort.bam
$samtools index test.anno.sort.filtered.sort.bam
[E::hts_idx_push] Unsorted positions on sequence #17: 63607429 followed by 63607391
samtools index: failed to create index for "test.anno.sort.filtered.sort.bam"
Try this:
sudo docker run -v pwd:/data blachlylab/fade annotate -b /data/test.bam /data/Homo_sapiens_assembly38.fasta > test.anno.bam
samtools sort -n test.anno.bam >test.anno.sort.bam
sudo docker run -v pwd:/data blachlylab/fade out -b -c /data/test.anno.sort.bam > test.anno.sort.filtered.bam
samtools sort test.anno.sort.filtered.bam >test.anno.sort.filtered.sort.bam
samtools index test.anno.sort.filtered.sort.bam
In order to index the bam you need to do a coordinate sort. samtools sort -n
is a queryname sort that is useful for fade out
. In order to index the output of fade out
you need to re-sort with samtools sort
without the -n
flag.
Thanks! It works.
Dear sir, I tried to use docker to process fade on my bam file, and the filtered bam cannot indexed by samtools so that I can't call somatic variants by mutect2. command I used: sudo docker run -v
pwd
:/data blachlylab/fade out -b -c /data/input.hg38.fade.bam >out.hg38.fade.filtered.bam samtools index out.hg38.fade.filtered.bam [E::hts_idx_push] Unsorted positions on sequence #1: 203008683 followed by 203008623 [E::sam_index] Read 'A00355:191:HJ2TWDSXY:2:1101:1009:14982' with ref_name='chr1', ref_length=248956422, flags=163, pos=2030dEven I use samtools sort. The same error keep coming.