Question: Freebayes tumor vs. normal inquiry
0
gravatar for alons
3.1 years ago by
alons270
Rehovot
alons270 wrote:

HI all,

I've been trying to run Freebayes variant caller on a pair of tumor-normal samples but I can't seem to get the bar column for the normal bam file or the tumor. The commands I tried were:

 freebayes -F 0.01 -C 2 --pooled-continuous --fasta-reference efgenome.fa tumor/aligned_sorted.bam normal/aligned_sorted.bam > var_bayes_tumor_normal.vcf

 freebayes -F 0.01 -C 2 --pooled-continuous --fasta-reference efgenome.fa tumor/aligned_sorted.bam -b normal/aligned_sorted.bam > var_bayes_tumor_normal.vcf

 freebayes -F 0.01 -C 2 --pooled-continuous --fasta-reference efgenome.fa -b tumor/aligned_sorted.bam -b normal/aligned_sorted.bam > var_bayes_tumor_normal.vcf

Each of them only gave me one bar column, for example:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bar

chr10 123240474 . G T 61.0498 . AB=0;ABP=0;AC=2... GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:77:-7.30883,-0.60206,0

I've read that Freebayes doesn't have a run option specifically for tumor-normal analysis but you can supply it with 2 bam files (or more) and do the analysis yourself. Has anyone succeeded in running freebayes on 2 bam files and getting 2 bar columns in the VCF or know how to interpret the VCF in regard to it's run on 2 separate bam files?

snp freebayes tumor ngs • 1.7k views
ADD COMMENTlink modified 2.8 years ago by sambrightman20 • written 3.1 years ago by alons270

Hi Herzliya, I am getting the same issue and looking out for solution. Did you get turn around this?

ADD REPLYlink written 2.8 years ago by shrutidesai02080
2
gravatar for sambrightman
2.8 years ago by
sambrightman20
Amsterdam
sambrightman20 wrote:

I believe this is caused by having the same ID field in the RG tag for the normal and tumour samples. Freebayes needs a unique sample ID, which I think is not always the case if samples were in the same run/lane. I reheader-ed by tumour BAM and got both columns in the output.

As far as I can tell the fact that Freebayes does this silently is a bug. It has a check for duplicate IDs and should exit with a message when they occur. However, it is ultimately relying on SamReadGroupDictionary for the combined headers, which silently discards read groups with the same ID before they reach Freebayes' check.

ADD COMMENTlink written 2.8 years ago by sambrightman20
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