I have received a VCF from LowFeq form a collaborator that used it for calling SNVs from a cfDNA targeted sequencing assay at a high depth of coverage. They develop scripts to use UMIs in the adapters to error correct the aligned reads and then produce a BAM file to feed to LowFreq. The aim is to detect somatic variants in the range of 0.5-2% VAF. However, it appears LowFreq not adding the PASS filter tag to variants under ~2% VAF. Further, since these variants are not passed, the genotypes are reported as 0/0 instead of 0/1 breaking some of our annotation piupeloines, Looking at the doucmentation is not clear if LowFreq has a minmum VAF threshold to pass a variant and if so, how can be changed, or if there is anothert issue that prevents the call. Can you let us know if there are paramters to force LowFreq to PAss variants in the above indicated VAF range? Thanks,
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LoFreq doesn't have an AF filter. The default filter is based on variant
quality only. It furthermore actually doesn't report genotypes. Taken
together this makes it likely that your collaborator post-processed the vcf
file somehow.
I have received a VCF from LowFeq form a collaborator that used it for
calling SNVs from a cfDNA targeted sequencing assay at a high depth of
coverage. They develop scripts to use UMIs in the adapters to error correct
the aligned reads and then produce a BAM file to feed to LowFreq. The aim
is to detect somatic variants in the range of 0.5-2% VAF. However, it
appears LowFreq not adding the PASS filter tag to variants under ~2% VAF.
Further, since these variants are not passed, the genotypes are reported as
0/0 instead of 0/1 breaking some of our annotation piupeloines, Looking at
the doucmentation is not clear if LowFreq has a minmum VAF threshold to
pass a variant and if so, how can be changed, or if there is anothert issue
that prevents the call. Can you let us know if there are paramters to force
LowFreq to PAss variants in the above indicated VAF range? Thanks,
I have received a VCF from LowFeq form a collaborator that used it for calling SNVs from a cfDNA targeted sequencing assay at a high depth of coverage. They develop scripts to use UMIs in the adapters to error correct the aligned reads and then produce a BAM file to feed to LowFreq. The aim is to detect somatic variants in the range of 0.5-2% VAF. However, it appears LowFreq not adding the PASS filter tag to variants under ~2% VAF. Further, since these variants are not passed, the genotypes are reported as 0/0 instead of 0/1 breaking some of our annotation piupeloines, Looking at the doucmentation is not clear if LowFreq has a minmum VAF threshold to pass a variant and if so, how can be changed, or if there is anothert issue that prevents the call. Can you let us know if there are paramters to force LowFreq to PAss variants in the above indicated VAF range? Thanks,
Hi Francisco,
LoFreq doesn't have an AF filter. The default filter is based on variant
quality only. It furthermore actually doesn't report genotypes. Taken
together this makes it likely that your collaborator post-processed the vcf
file somehow.
Hope this helps,
Andreas
On 24 March 2018 at 13:45, Francisco De La Vega ribozyme@users.sourceforge.net wrote:
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Andreas Wilm
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