strange output when trying to get consensus from a sorted bam file
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4.7 years ago
lait ▴ 160

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

bam consensus NGS samtools • 1.1k views
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What version of samtools and bcftools do you have?

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both have version 1.3.1

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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 ?

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