/samtools-1.2/samtools mpileup -d 8000 -q 25 -Iu -f reference.fasta sample.sorted.bam > sample.pileup &
using the above command line gives the prompt as below:[mpileup] 1 samples in 1 input files
Is it an error or I can ignore it and continue with the downstream pipeline?
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written
by
linzhang •
2 answers
That's informational. As it says, you specified one file that has one sample in it for variant calling.
One possible cause is that the default mpileup ignores the non-properly paired reads, which could mean sometimes all reads in the alignment get ignored. Adding -A option would override the default behavior and report non-properly paired reads. Also see the following link: http://seqanswers.com/forums/archive/index.php/t-9717.html
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Hello everyone i also having same problem please anyone can help i am using sorted.bam file to call variants
As I wrote in reply to this four months ago, that's just informational. It's not a problem or an error. If you have an actual error of some sort, please post a new question.
But i didn't got vcf file the error file show this message, and the process fail further
Right, so it prints a bit of information to standard error (where information is normally printed) and then quits. Post more details in a new question.
enter link description here
Link refers to this same page?