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
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What version of samtools and bcftools do you have?
both have version 1.3.1
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 ?