This tool generates Fasta files out of variant (SNP) alignments or full alignments (consensus). It can be very useful to produce the right input needed for follow up tools, for example phylogenetic tree building.
BastyGenerateFasta requires Java 8 to be installed on your device. Download Java 8 here or install via your distribution's package manager.
Download the latest version of BastyGenerateFasta here. To generate the usage run:
java -jar <BastyGenerateFasta_jar> --help
BastyGenerateFasta has three modes:
Minimal example for option: --outputVariants
(VCF based)
java -jar <BastyGenerateFasta_jar> \
--inputVcf myVCF.vcf \
--outputName NiceTool \
--outputVariants myVariants.fasta
Minimal example for option: --outputConsensus
(BAM based)
java -jar <BastyGenerateFasta_jar> \
--bamFile myBam.bam \
--outputName NiceTool \
--outputConsensus myConsensus.fasta \
--reference reference.fa
Minimal example for option: --outputConsensusVariants
(Both)
java -jar <BastyGenerateFasta_jar> \
--inputVcf myVCF.vcf \
--bamFile myBam.bam \
--outputName NiceTool \
--outputConsensusVariants myConsensusVariants.fasta \
--reference reference.fa
Usage for BastyGenerateFasta:
Option | Required | Can occur multiple times | Description |
---|---|---|---|
--log_level, -l | no | no | Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error' |
--help, -h | no | no | Print usage |
--version, -v | no | no | Print version |
--inputVcf, -V | no | no | vcf file, needed for outputVariants and outputConsensusVariants |
--bamFile | no | no | bam file, needed for outputConsensus and outputConsensusVariants |
--outputVariants | no | no | fasta with only variants from vcf file |
--outputConsensus | no | no | Consensus fasta from bam, always reference bases else 'N' |
--outputConsensusVariants | no | no | Consensus fasta from bam with variants from vcf file, always reference bases else 'N' |
--snpsOnly | no | no | Only use snps from vcf file |
--sampleName | no | no | Sample name in vcf file |
--outputName | yes | no | Output name in fasta file header |
--minAD | no | no | min AD value in vcf file for sample. Defaults to: 8 |
--minDepth | no | no | min depth in bam file. Defaults to: 8 |
--reference | no | no | Indexed reference fasta file |
BastyGenerateFasta is part of BIOPET tool suite that is developed at LUMC by the SASC team. Each tool in the BIOPET tool suite is meant to offer a standalone function that can be used to perform a dedicate data analysis task or added as part of BIOPET pipelines.
All tools in the BIOPET tool suite are Free/Libre and Open Source Software.
The source code of BastyGenerateFasta can be found here. We welcome any contributions. Bug reports, feature requests and feedback can be submitted at our issue tracker.
BastyGenerateFasta is build using sbt. Before submitting a pull request, make sure all tests can be passed by
running sbt test
from the project's root. We recommend using an IDE to work on BastyGenerateFasta. We have had
good results with this IDE.
For any question related to BastyGenerateFasta, please use the github issue tracker or contact the SASC team directly at: sasc@lumc.nl.