Entering edit mode
6.6 years ago
hdtms
▴
20
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?
what is your GATK version ? re-test with a recent version.
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.