Question: No RS id was called in vcf file after giving dbsnp command
gravatar for Kritika
9 weeks ago by
Kritika250 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 • 167 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Kritika250

i tried running SNP calling step

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ADD REPLYlink written 9 weeks ago by Pierre Lindenbaum105k

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

ADD REPLYlink written 5 weeks ago by mittu1602140
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