Error in SNP calling using samtools and bcftools
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6.5 years ago

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

SNP RNA-Seq • 5.4k views
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1
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Maybe A: SNP call using bcftools post is interesting for you?

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6.5 years ago

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

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Entering edit mode
6.5 years ago

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

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@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

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6.1 years ago
ricket.woo • 0

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

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