Question: Varscan Error On Mpileup Input
0
gravatar for GPR
6.4 years ago by
GPR310
Mexico
GPR310 wrote:

Hello, I am trying to filter low quality data off my mpileup files using Varscan but keep getting stuck with the error message: Invalid format for pileup at line 1. I don't think my vcf tools are corrupted, since they have made it through bedtools instersect.

The command lines I have used are the following:

samtools mpileup -uf genome.fa 1.bam 2.bam | bcftools view -bvcg -> *.bcf

I also used -vcg -> *.vcf and even ommitted -u. For VarScan I am typing:

java -jar VarScan.jar mpielup *.vcf  --output-vcf

Any tip to as why is my vcf file not recognized by VarScan will be appreciated.

varscan • 4.2k views
ADD COMMENTlink modified 6.4 years ago by dankoboldt140 • written 6.4 years ago by GPR310
1
gravatar for Irsan
6.4 years ago by
Irsan6.8k
Amsterdam
Irsan6.8k wrote:

Do you want to convert the samtools mpileup format to variant calls and filter them for variant allele frequency, #reads supporting variant/reference, etc? Then the command you should use is

samtools mpileup -uf genome.fa 1.bam 2.bam | java -jar /path/to/VarScan.jar mpileup2snp --output-vcf > your_sample.vcf

So not

java -jar VarScan.jar mpielup *.vcf --output-vcf

So, it expects a .pileup-file, not vcf

ADD COMMENTlink modified 6.4 years ago by Istvan Albert ♦♦ 80k • written 6.4 years ago by Irsan6.8k

Thanks, I went ahead with your recommendation, but I get the same error: invalid format at line 1. My bam files have a header, are sorted, and the duplicates removed.I also tried adding Read Groups, which are needed to get GATK working. Any other suggestions?

ADD REPLYlink written 6.4 years ago by GPR310

The job actually went through when taking -u off in samtools mpileup . Thanks again!

ADD REPLYlink written 6.4 years ago by GPR310

Nice you have sorted it out!

ADD REPLYlink written 6.4 years ago by Irsan6.8k
1
gravatar for dankoboldt
6.4 years ago by
dankoboldt140
dankoboldt140 wrote:

Irsan, thanks for helping out!

ADD COMMENTlink written 6.4 years ago by dankoboldt140
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