Question: (Closed) GATK HaplotypeCaller error ?
0
gravatar for Ramana
2.3 years 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 • 1.4k views
ADD COMMENTlink modified 13 months ago • written 2.3 years 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 2.3 years ago by Pierre Lindenbaum127k

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.

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

Cheers!

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum127k

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 2.3 years ago by Pierre Lindenbaum127k
0
gravatar for WouterDeCoster
2.3 years ago by
Belgium
WouterDeCoster43k 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 2.3 years ago by WouterDeCoster43k
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