Question: To Avoid The 'Argument "F" Isn'T Numeric In Numeric
0
gravatar for Zhshqzyc
7.3 years ago by
Zhshqzyc470
Zhshqzyc470 wrote:

Hello, I am running the command like:

samtools mpileup -uf hg18.fa my.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

However I got many many warnings on the screen which are like

Argument "chr1^I22217285^I.^IT^I.^I28.2^I.^IDP=1;;CI95=1.5,0;FQ=-3..." isn't numeric in numeric lt (<) at /mypath/samtools/bcftools/vcfutils.pl line 503, <> line 21409998.
Argument "chr1^I22250317^I.^IT^I.^I28.2^I.^IDP=9;;CI95=1.5,0;FQ=-3..." isn't numeric in numeric lt (<) at /Mypath/samtools/bcftools/vcfutils.pl line 503, <> line 21443057.

What is wrong and how to avoid it? My reference fa file likes

>chr10

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Thanks.

perl samtools • 2.8k views
ADD COMMENTlink modified 11 weeks ago by Biostar ♦♦ 20 • written 7.3 years ago by Zhshqzyc470

It works on a BAM file for me - how did you make your BAM file. ^I is often a tab - or "t" in perl.

ADD REPLYlink written 7.3 years ago by Chris Penkett470
1
gravatar for Swbarnes2
7.2 years ago by
Swbarnes21.4k
Swbarnes21.4k wrote:

Come on. You have to try a little. If you are having trouble with a command that pipes a whole bunch of commands together, you have to split them apart, to figure out which command is the problem. Given that the problem looks like mpileup is balking at your .bam file, you really ought to convert some of it to .sam, and put up the first few offending lines of the .sam.

ADD COMMENTlink written 7.2 years ago by Swbarnes21.4k
0
gravatar for Pierre Lindenbaum
7.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k wrote:

(not tested) samtools mpileup is missing the option -g ("generate BCF output ") ?

ADD COMMENTlink written 7.3 years ago by Pierre Lindenbaum116k

I tried the command samtools mpileup -uf hg18.fa -g my.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq But it still failed. Can you list your command?

ADD REPLYlink written 7.3 years ago by Zhshqzyc470
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