Question: No RS id was called in vcf file after giving dbsnp command
gravatar for Kritika
11 months ago by
Kritika260 wrote:

Hi I have DBSNP VCf file for my genome i used GATK for variant calling with option -d dbsnp.vcf No RS id were reported in my out.vcf . That means all my SNP in out.vcf is novel !?

Then i edited my dbsnp.vcf chromosome name same like my ref.fasta and bam file rerun GATK using this edited dbsnp.vcf. It gave me error saying "The provided VCF file is malformed at approximately line number 15: 0 is an invalid filter name in vcf4"

Will it be possible not to get any reported snps from dbsnp.vcf in my out.vcf ? Also what the above error means?

snp dbsnp no match • 467 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Kritika260

i tried running SNP calling step

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ADD REPLYlink written 11 months ago by Pierre Lindenbaum115k

Please post your GATK command, and please be careful of your post

ADD REPLYlink written 10 months ago by mittu1602150
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