/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?
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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version 2.3.6
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.
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Link refers to this same page?