Error in SNP calling using samtools and bcftools
3
0
Entering edit mode
6.4 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]$samtools mpileup -uf BRP.fas RMR1_sub_1000000_1_mit.sort.bam RMR1_sub_1000000_2_mit.sort.bam | bcftools view -vcg - > BRP.Chr01.vcf [mpileup] 2 samples in 2 input files <mpileup> Set max per-file depth to 4000 [E::cg] unknown type I try to different computers and still met the error. Best ZQ SNP RNA-Seq • 5.3k views ADD COMMENT 1 Entering edit mode Maybe A: SNP call using bcftools post is interesting for you? ADD REPLY 0 Entering edit mode 6.4 years ago You don't want the -v option, that's what's causing this to happen. ADD COMMENT 0 Entering edit mode 6.4 years ago Hi Ryan, I try your suggestion, but I still have the error like: bash-3.2$ 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

0
Entering edit mode

@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

0
Entering edit mode
6.0 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.