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VariantsToVCF GATK toolkit

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!

bam gatk vcf
• 3,357 views • link
updated by Ram Ram • written by Maria333 • Maria333

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

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updated by Ram Ram • written by GouthamAtla GouthamAtla

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!

• 0 views • link
updated by Ram Ram • written by Maria333 • Maria333

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