BAM to VCF conversion

[vd4mindia]

Thank you for the valuable thread. I have some more query for which I need some suggestions, I am new to GATK and want to use it for my exome sequencing data analysis. I have been a bit lost reading all the blogs , comments and the technical forums. So here is something I want to say and please correct and guide me through the procedure. I have downloaded the hg19 files from the UCSC browser and created the reference genome but do I need to again use the one which is there in GATK repository and then align my samples for downstream analysis? Also I want to run the GATK in my institute cluster. So if am not wrong I should create the directory of the latest GATK version and transfer all the necessary files via Filezilla in the cluster directory with the same name. Now this I have already done. So next thing is to download the bundle from the repository where I see 2 versions , so which one should I download? 2.5 or 2.3? Also once I download the bundle do I have to download anything else? So here it is which I should be downloading right in my cluster. The jar file and the resource folder with the .java files and then in the main directory of the GATK version folder in my cluster I should download the bundle version (2.5 or 2.3) and then unzip all the files that are there in the bundle directory. Right? Please let me know. Then I should be ready to use the GATK for the different downstream processes listed below:

Identify target regions for realignment (Genome Analysis Toolkit) ->Realign BAM to get better Indel calling (Genome Analysis Toolkit) ->Reindex the realigned BAM (SAM Tools) ->Call Indels (Genome Analysis Toolkit) ->Call SNPs (Genome Analysis Toolkit)->View aligned reads in BAM/BAI (Integrated Genome Viewer)

Please let me know if this looks correct or not. The VCF files from the 1kG and the DBSNP are already there in compressed form in the bundle repository of the GATK website which I am currently downloading and I can use them directly after unzipping them.

[ashwatha]

Thanks, Ketan and Peter!

[ulz_peter]

I'd recommend GATK as well:

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

like mentioned in my post above VarScan would be another option: http://varscan.sourceforge.net/

[ketan_bnf]

You can use samtools mpileup option, visit this link

http://samtools.sourceforge.net/mpileup.shtml

also you can use GATK for variant calling.

[ashwatha]

Hi Peter,

I see what you mean - my question was not worded correctly. What I am looking for is a way to take a BAM file, and call variants on it and generate a VCF file, the way "samtools pileup" generates a pileup file out of a BAM file.

If such a tool doesn't exist, I could also use something that can convert a pileup file generated using samtools pileup to a VCF file, considering that pileup files and VCF files contain similar data (at least for coordinates where there is a SNP or other variant).

thanks,
Ashwatha.

[ulz_peter]

I can't see why you want to convert a BAM file to a vcf file. The Bam file stores the alignment where the VCF file stores variants. In order to generate a vcf file you would need to do a proper SNP calling (e.g. GATK, VarScan, ...). A direct conversion makes no sense for me...

[ashwatha]

Hi,

are there any tools to convert BAM files to VCF (Variant Call Format)? Alternatively, are there any tools to convert pileup files to VCF?

Looking at the VCF specs, VCF is fairly similar to pileup format, so I can probably write a script for this conversion. I am just wondering if something already exists.

Any pointers are much appreciated!

thanks,
Ashwatha.