VariantsToVCF GATK toolkit

Question

[Maria333]

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!

[GouthamAtla]

Are you sure -R example.bam.bai? I guess -R should point to reference.

[Maria333]

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:

This argument supports ROD files of the following types: BCF2,BEAGLE, BED, BEDTABLE, EXAMPLEBINARY, GELITEXT, RAWHAPMAP, REFSEQ, SAMPILEUP, SAMREAD, TABLE, VCF, VCF3

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!