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Bam not accepted by HaplotypeCaller

sgoyalsgoyal San CarlosMember

Hi there,

Simulated some reads. My bam has around 400 reads.. trying to run haplotypecaller but getting error. Need help

$ java -jar $GATK -T HaplotypeCaller -R ucsc.hg19.fasta -I pex_defaults_RG.bam  -o pex.vcf

ERROR MESSAGE: Invalid command line: The GATK reads argument (-I, --input_file) supports only BAM/CRAM files with the .bam/.cram extension and lists of BAM/CRAM files with the .list extension, but the file pex_defaults_RG.bam  has neither extension. Please ensure that your BAM/CRAM file or list of BAM/CRAM files is in the correct format, update the extension, and try again.

I checked file manually and validated using picard - it looks ok .. any thoughts ?

$ java -jar $PICARD ValidateSamFile I=pex_defaults_RG.bam MODE=SUMMARY

[Mon Oct 03 15:12:06 PDT 2016] picard.sam.ValidateSamFile INPUT=pex_defaults_RG.bam MODE=SUMMARY MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Mon Oct 03 15:12:06 PDT 2016] Executing as [email protected] on Mac OS X 10.10.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_65-b17; Picard version: 1.141(8ece590411350163e7689e9e77aab8efcb622170_1447695087) JdkDeflater
No errors found
[Mon Oct 03 15:12:06 PDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=257425408

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