Question: Error in SNP calling using samtools and bcftools
0
gravatar for wu.zhiqiang.1020
3.4 years ago by
United States
wu.zhiqiang.102020 wrote:

Dear all,

I am using the newest version of samtools and bcftools (Version: 1.2 (using htslib 1.2.1)) to call the snps from sorted Bam files, but I have error all the time. I try to search online, but no clear answer about this, Could anyone can help me to figure out this?

this is the commands what I used:

[wu@correns RMR1_subsample_1000000]$ samtools mpileup -uf BRP.fas RMR1_sub_1000000_1_mit.sort.bam RMR1_sub_1000000_2_mit.sort.bam | bcftools view -vcg - > BRP.Chr01.vcf


[mpileup] 2 samples in 2 input files
<mpileup> Set max per-file depth to 4000
[E::cg] unknown type

I try to different computers and still met the error.

Best

ZQ

rna-seq snp • 3.4k views
ADD COMMENTlink modified 3.0 years ago by ricket.woo0 • written 3.4 years ago by wu.zhiqiang.102020
1

Maybe A: SNP call using bcftools post is interesting for you?

ADD REPLYlink written 3.4 years ago by iraun3.4k
0
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan85k
Freiburg, Germany
Devon Ryan85k wrote:

You don't want the -v option, that's what's causing this to happen.
 

ADD COMMENTlink written 3.4 years ago by Devon Ryan85k
0
gravatar for wu.zhiqiang.1020
3.4 years ago by
United States
wu.zhiqiang.102020 wrote:

Hi Ryan,

I try your suggestion, but I still have the error like:

bash-3.2$ samtools mpileup -uf BRP.fas RMR1_sub_1000000_1_mit.sort.bam RMR1_sub_1000000_2_mit.sort.bam | bcftools view -cg - > RMR1_sub_1000000.raw.bcf  

Error: Could not parse --min-ac g

[mpileup] 2 samples in 2 input files

<mpileup> Set max per-file depth to 4000

If I use the old version of the samtools and bcftools, it works and no error. What's the problem?

 

ZQ

ADD COMMENTlink written 3.4 years ago by wu.zhiqiang.102020

@ZQ you should mark your code as proper code. it makes it easier to read. Also have a good look at the lilnk posted by airan. bcftools have changed. You no longer call variants with `bcftools view` instead `bcftool call`. Here is another link A: Samtools mpileup quality scores all zero

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Kirill250
0
gravatar for ricket.woo
3.0 years ago by
ricket.woo0
China
ricket.woo0 wrote:

You'd better change using an older version of bcftools and samtools, since the options -v -c -g are of different meaning now.

ADD COMMENTlink written 3.0 years ago by ricket.woo0
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