vcf to maf conversion & cloud application
Hi,
I am new to bioinformatics and I am given the attached vcf file. I would like to convert vcf files to maf format.
I also received SNP annotated file with impact and potential GO function and clinVAR relevance (in an excel format for each sample).
I would like to use these files to do further analysis and generate plots using MAFtools.
1 - Could you please suggest which tool I could use to do the vcf to maf conversion?
2 - Could you suggest if it is possible to use GATK pipeline (Terra / IBM cloud...) on cloud from bam file to plots to analyse whole genome/amplicon sequencing data and the cost it would incur?
Your expert suggestion will be very helpful. Thank you.
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Hi Ravi
We don't have a default tool to make VCF to MAF conversion however Funcotator tool can output MAF format which may still not work for your case since MAF format is also not very well standardized.
You are welcome to use GATK workflows stored in Terra or IBM cloud. Costs depend many different parameters and file localization needs but you may be able to see some estimates once you start checking the workflows.
Regards.
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Dear Gokalp,
Thank you for your expert reply. In that case, may I know which other tools I could use to generate plots from target seq data ?
I will check GATK pipeline on Terra.
Best Regards,
Ravi.
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Hi again.
There are a bunch of tools out there however it is not easy to recommend one directly. You may want to check google and biostars forums for better information on that. As I said Funcotator can also produce MAF output if you wish to annotate your VCFs and generate an annotated MAF.
Regards.
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Thank you, Celik. I will check Funcotator's code/package to run on Terra.
Best,
Ravi.
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Dear Celik,
I am checking the Funcotator's documentation on terra. Could you please suggest the columns needed for VCF to MAF conversion? Is it enough if I include gene name, and position while preparing the csv file from VCF (which I already have) or is it necessary to include any other columns like dbSNP id / REF / ALT allele information? Your expert suggestion would help.
Thank you.
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Hi Ravi
Sorry for my late response. I am not really expert on MAF format and its use cases however columns would certainly be dependent on what you would like to see in your final data I guess.
Regards.
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Thank you, Celik.
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