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.
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written
by
GPR
2 answers
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
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written
by
Irsan
Irsan, thanks for helping out!
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