No depth information in INFO column

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Jay Singh

• May 16, 2020 20:52

Can you please provide
a) GATK version used-  4.1.7.0
b) Exact GATK commands used -

./gatk --java-options "-Xmx4g" HaplotypeCaller \
-R /media/deepak/EXTRA/Genomedir/hg38/hg38.fasta \
-I /media/deepak/EXTRA/Genomedir/sample3_bqsr.bam \
-O SAMPLE3_Haplo.g.vcf.gz \
-ERC GVCF \
-G Standard \
-G AS_Standard

c) The entire error log if applicable.

I have used HAPLOTYPE CALLER for variant calling from RNA Seq Data.

However variant depth information is missing from the INFO column in the output vcf file.

How to get the depth information in the INFO column?

I cannot able to run RNAseqCNV package wihout the depth information.

Kindly help.

Thanks and Regards.

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  David Benjamin

  • May 17, 2020 03:38

  Jay Singh Your command generates a GVCF.  If you are doing joint calling, you must merge the single-sample GVCFs with GenotypeGVCFs.  If you are doing single-sample calling you should remove -ERC GVCF from your command.

  I'm guessing that the DP INFO field is missing from the "reference block" GVCF lines where the only alt allele is <NON-REF>, but present in all others.  If so, everything will be fine after GenotypeGVCFs.

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  Jay Singh

  • May 17, 2020 19:38

  Dear David

  Thanks for the reply.

  Yes You are right. DP INFO field is missing from the "reference block" GVCF lines where the only alt allele is <NON-REF>, but present in all others.

  Thanks.

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