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joint calling #6
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Yes, joint calling is done in that way. See also the example in README: fermi.kit/htsbox pileup -cuf ref.fa pre1.srt.bam pre2.srt.bam > out.raw.vcf
fermi.kit/k8 fermi.kit/hapdip.js vcfsum -f out.raw.vcf > out.flt.vcf The second command line filters the calls. Please note that |
Thanks, I'm using it for denovo calling in trios. |
I am afraid that wouldn't work well, either. The problem with fermikit is that when it misses a variant, it misses completely. FNs in parents will lead to spurious de novo calls. In comparison, when a typical caller (e.g. gatk/samtools) misses a variant, you can usually see a few reads having the correct variants. This helps to reduce false de novo calls. Probably the right way to perform normal-tumor and trio calling is to assemble the tumor/child and then map it against error corrected reads of normal/parents with |
PS: alternatively, you can use both fermikit and a typical de novo calling pipeline at the same time. You may require a de novo variant called by both approaches. Fermikit uses a very different method for variant calling. Combing distinct approaches usually helps to reduce false positives. |
I see, I had not considered the FN issue and just thought the low FDR would be helpful. I will have a play around with your suggestions. |
Hi Heng,
Great tool. Do you have any advice for joint calling of multiple samples?
I obtained a reasonable looking call set by first running your
run-calling
script on each sample individually. Then I ran the following on the bams produced:fermi.kit/htsbox pileup -cuf hs37d5.fa *.bam | bcftools view -Oz output.vcf.gz
Is this a sensible approach? Obviously filtering still needs to performed.
cheers,
Jared
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