Question: [mpileup] 1 samples in 1 input files Is it an error?
0
gravatar for linzhang
2.7 years ago by
linzhang0
linzhang0 wrote:

/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?

snp • 1.5k views
ADD COMMENTlink modified 8 weeks ago by Vitis1.7k • written 2.7 years ago by linzhang0

Hello everyone i also having same problem please anyone can help i am using sorted.bam file to call variants

ADD REPLYlink written 2.3 years ago by Aamiralizai0

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.

ADD REPLYlink written 2.3 years ago by Devon Ryan86k

But i didn't got vcf file the error file show this message, and the process fail further

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Aamiralizai0

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.

ADD REPLYlink written 2.3 years ago by Devon Ryan86k

enter link description here

ADD REPLYlink written 2.3 years ago by Aamiralizai0

Link refers to this same page?

ADD REPLYlink written 2.3 years ago by WouterDeCoster35k
1
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

That's informational. As it says, you specified one file that has one sample in it for variant calling.

ADD COMMENTlink written 2.7 years ago by Devon Ryan86k
0
gravatar for Vitis
8 weeks ago by
Vitis1.7k
New York
Vitis1.7k wrote:

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

ADD COMMENTlink written 8 weeks ago by Vitis1.7k
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