Question: GATK Indel sorting, vcf error
0
gravatar for hdtms
2.2 years ago by
hdtms 20
hdtms 20 wrote:

Hi I used the GATK pipeline until I got a vcf that had SNPs and Indels, so I used GATK Analysis tools to remove SNPs and keep Indels. But after adding the reference genome, dictionary and index I get this error:

The provided VCF file is malformed at approximately line number 455: Unparsable vcf record with allele *, for input source: /home/helenadarmancier/Documents/Estagio/Original/vcf_NoAngH201_NoMono.vcf

How can I fix this?

snp software error • 791 views
ADD COMMENTlink written 2.2 years ago by hdtms 20

what is your GATK version ? re-test with a recent version.

ADD REPLYlink written 2.2 years ago by Pierre Lindenbaum124k

Hello hdtms !

It appears that your post has been cross-posted to another site: https://gatkforums.broadinstitute.org/gatk/discussion/10363/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum124k
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