Hi,
I used the following SNVer command for printing out putative variants in VCF format:
java -Xmx4g -jar ~/SNVer-0_4_1/SNVerIndividual.jar \
-i bamfile.bam \
-r hg19_ucsc.fasta \
-o output_SNVer \
-db ~/data/db_SNP/snp135.txt,2,4,5
the output_SNVer.raw.vcf and output.SNVer.filter.vcf files that I obtain does contains "." for Qval column while the rest looks fine. Is there anyway I get Qvals in output?
Nothing is wrong with input bam file since when I ran mpileup on the same bam file I get Qval values for variants in output vcf.
I used the following SNVer command for printing out putative variants in VCF format:
java -Xmx4g -jar ~/SNVer-0_4_1/SNVerIndividual.jar \
-i bamfile.bam \
-r hg19_ucsc.fasta \
-o output_SNVer \
-db ~/data/db_SNP/snp135.txt,2,4,5
the output_SNVer.raw.vcf and output.SNVer.filter.vcf files that I obtain does contains "." for Qval column while the rest looks fine. Is there anyway I get Qvals in output?
Nothing is wrong with input bam file since when I ran mpileup on the same bam file I get Qval values for variants in output vcf.
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