Unable to run Picard GtcToVcf

Follow

Damian Fermin

• September 08, 2022 14:03

I have a GTC file I'd like to convert to a VCF file using Picard's GtcToVcf funcionality.

a) Picard version: 2.27.4-SNAPSHOT

b) Exact command:

java -Xmx32g -jar /usr/local/bin/picard.jar GtcToVcf \
  INPUT=40037.gtc \
  REFERENCE_SEQUENCE=/genomes/human/hs37d5.fa \
  OUTPUT=40037.vcf \
  CLUSTER_FILE=../ClusterFile/InfiniumCoreExome-24v1-4_A1_ClusterFile.egt \
  MANIFEST=../Manifest/InfiniumCoreExome-24v1-4_A1.csv \
  BPM_FILE=..//Manifest/InfiniumCoreExome-24v1-4_A1-bpm/InfiniumCoreExome-24v1-4_A1.bpm \
  SAMPLE_ALIAS=samp1 \  
  TMP_DIR=/scratch

c) The program does not run but issues this message at the end:

The selected reference sequence ('b37') is not supported.  This tool is currently only implemented to support NCBI Build 37 / HG19 Reference Sequence.

I tried recreating the fasta file dictionary with multiple values for --GENOME_ASSEMBLY in Picard's CreateSequenceDictionary command. None seem to satisfy the GtcToVcf command.

Any suggestions are welcome.

 

0

• 

  Genevieve Brandt (she/her)

  • September 08, 2022 18:39

  Thank you for your post, Damian Fermin! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

  0

  Comment actions Permalink
• 

  Nur Adlina Binti Mohd Affian

  • July 29, 2024 08:34

  Hi Genevieve Brandt (she/her) , I found that this question have been resolve as I also facing the same error while running the script with GRCh38 reference. May I know, is there any alternative approach to resolve this issue ? 

  0

  Comment actions Permalink
• 

  Gökalp Çelik

  • July 29, 2024 08:48

  Hi Nur Adlina Binti Mohd Affian

  Your best option is to use a GRCh38 reference genome that has contig names starting with chr prefix. Also you need to check all manifest files to see if they are compatible with GRCh38 or not. 

  Please make sure that you are using the latest version of Picard for this purpose. If none of them works as expected please check the documentation and software provided by Illumina to convert Gtc files to VCF 

  https://github.com/Illumina/GTCtoVCF 

  https://support.illumina.com/array/array_software/dragen-array-secondary-analysis/downloads.html

  0

  Comment actions Permalink

Please sign in to leave a comment.