Question: (Closed) GATK HaplotypeCaller error ?
0
gravatar for Ramana
17 months ago by
Ramana0
Ramana0 wrote:

Hi, I tried to generated a .VCF file using GATK HaplotypeCaller. I provided all the input requirements hg38.fa, hg38.dict, hg38.fa.fi and Bam file. Java 1.8 and picard

I'm getting this error, kindly reply.

Command : java -jar GenomeAnalysisTK.jar HaplotypeCaller -R /home/Downloads/GenomeAnalysisTK-3.8-0-ge9d806836/hg38.fa -I /media/CANCERGENOMICS/NA12878.bam -o /home/Downloads/GenomeAnalysisTK-3.8-0-ge9d806836/NA12878GATK.vcf

INFO 12:15:43,860 HelpFormatter - ---------------------------------------------------------------------------------- INFO 12:15:43,862 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50

alignment genome • 900 views
ADD COMMENTlink modified 10 weeks ago • written 17 months ago by Ramana0

it's a common error (e.g: GATK: Input files reads and reference have incompatible contigs: No overlapping contigs found ) , as the message said:

Input files reads and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information.

I'm closing this one.

ADD REPLYlink written 17 months ago by Pierre Lindenbaum119k

Hello pinnintilikithreddy!

We believe that this post does not fit the main topic of this site.

duplicate

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

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Cheers!

ADD REPLYlink written 17 months ago by Pierre Lindenbaum119k

Hello pinnintilikithreddy!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: duplicate
ADD REPLYlink written 17 months ago by Pierre Lindenbaum119k
0
gravatar for WouterDeCoster
17 months ago by
Belgium
WouterDeCoster38k wrote:

The chromosomes in the bam and the chromosomes in the reference genome don't match. Did you do the alignment or did you download the data from somewhere?

ADD COMMENTlink written 17 months ago by WouterDeCoster38k
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