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 sgoyal@sgoyal-mac2.local 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