Question: strange output when trying to get consensus from a sorted bam file
0
gravatar for lait
3.8 years ago by
lait150
lait150 wrote:

I used the following command:

samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.pl vcf2fq > cns.fq

to create the consensus of a sorted bam file.

strange letters appear ar the end of the output file cns.fq:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~z~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~x~uuuxx~~~~~~a~~~~~~~}~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~{xxxxuuuuror~~~~~~~~~~~~~~~~~~~~~~x~~~~~~~~~~~~~rK?

This spans to a huge number of lines. is this normal ? What does this mean ?

Note: this questions was asked by me in a comment in another post: C: get a consensus out of a Sorted bam file

samtools bam ngs consensus • 1.0k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by lait150

What version of samtools and bcftools do you have?

ADD REPLYlink written 3.8 years ago by Devon Ryan95k

both have version 1.3.1

ADD REPLYlink written 3.8 years ago by lait150

if I try htsbox , I get a file that contains just the letter X , like the following:

gi|556550243|ref|NC_022648.1|

nnnXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX etc

can anyone figure out the problem please ?

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by lait150
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