How to compare a tumour sample to multiple normal samples in Freebayes
1
2
Entering edit mode
5.4 years ago
nanana ▴ 110

I'm currently running Freebayes on tumour normal pairs to detect somatic SNPs in the tumour sample:

Raw germline calls:

freebayes -f genome.fa --pooled-discrete --genotype-qualities --read-mismatch-limit 70 \
tumour.bam normal.bam -v tn_raw.vcf

Decompose complex events into single SNPs and, tag the tumour and normal samples and quality-filter:

vcfallelicprimitives tn_raw.vcf | \
vt decompose_blocksub - | \
vt normalize -q -r genome.fa - | \
vcfsamplediff -s VT normal tumour - | \
vcffilter -f "DP > 20" \
-f "QUAL > 1 & QUAL / AO > 10" \
-f "SAF > 0 & SAR > 0" \
-f "RPR > 0 & RPL > 0" \
-f "TYPE = snp" > tn_snps_filt.vcf

Filter for somatic SNPs

vcffilter -f "VT = somatic" tn_snps_filt.vcf > tn_snps_somatic_filt.vcf

I would like to be able to include a panel of normals, and exclude any SNPs called as somatic that are present in any of the normal samples. I know that you can supply Freebayes with multiple samples, but how can I feed this information into vcfsamplediff?

next-gen snp genome • 2.1k views
ADD COMMENT
0
Entering edit mode
5.3 years ago

I believe you mean to filter in somatic SNPs and filter out germline SNPs. Using multiple normal samples is often known as a pool or panel of normals. More about that here. I looked around a bit at Freebayes and couldn't find anything directly from them. Looks like bcbio supports pooled normals via Freebayes though. You should check out MuTect - they are pretty commonly used and have pretty good documentation of pooled normals creation.

ADD COMMENT
0
Entering edit mode

I appreciate the comment, but this has got nothing to do with the question - of how to include a PON in Freebayes

ADD REPLY

Login before adding your answer.

Traffic: 1952 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6