Entering edit mode
9.2 years ago
Maria333
▴
20
Hi,
Does anyone know whether we are allowed to use bam files as the "variant file to convert" to VariantsToVCF on GATK toolkit?
I'm using the following command line:
java -jar ../GenomeAnalysisTK.jar -T VariantsToVCF -R example.bam.bai -o output.vcf -V example.bam
and I get:
Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
##### ERROR BEAGLE BeagleFeature (this is an external codec and is not documented within GATK)
##### ERROR BED BEDFeature (this is an external codec and is not documented within GATK)
##### ERROR BEDTABLE TableFeature (this is an external codec and is not documented within GATK)
##### ERROR EXAMPLEBINARY Feature (this is an external codec and is not documented within GATK)
##### ERROR GELITEXT GeliTextFeature (this is an external codec and is not documented within GATK)
##### ERROR RAWHAPMAP RawHapMapFeature (this is an external codec and is not documented within GATK)
##### ERROR REFSEQ RefSeqFeature (this is an external codec and is not documented within GATK)
##### ERROR SAMPILEUP SAMPileupFeature (this is an external codec and is not documented within GATK)
##### ERROR SAMREAD SAMReadFeature (this is an external codec and is not documented within GATK)
##### ERROR TABLE TableFeature (this is an external codec and is not documented within GATK)
##### ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
##### ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
Any help will be much appreciated.
Thank you!
Are you sure
-R example.bam.bai
? I guess-R
should point to reference.Actually
-R
is usually used when a .fasta file is followed, but I tried the .bam.bai as well. The instructions say that only the following can be used for the-V
option:But since the guide says that we can convert bams to vcf files, I thought that there might be a way of doing that and I just can't find it anywhere! The guide also suggests we can convert a .bam into a fasta format so again, it seems like it should do this.
Thanks anyway!