Comments (4)
Please use the command line in README for variant calling:
fermi.kit/run-calling -t16 bwa-indexed-ref.fa prefix.mag.gz | sh
GATK won't work well.
from fermikit.
Also to generate multi-sample vcf, first mapping and sort with fermi.kit/bwa mem -x intractg ref.fa unitigs.mag.gz && fermi.kit/htsbox samsort
and then do calling with:
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
See also README.
from fermikit.
Thank you! Just to clarify, GATK was used in order to compare the results of mapping raw reads and mapping unitigs, without having the extra confound of using different variant callers.
from fermikit.
Unitigs have very different characteristics from short reads. Most existing tools won't play well with unitigs.
from fermikit.
Related Issues (19)
- FYI - tar files created on OSX give wierd messages on Linux HOT 1
- Can FermiKit be run on Amplicon data from targeted re-sequencing HOT 1
- Call SV jointly? HOT 1
- using fermikit to generate a reference graph HOT 4
- Classify complex SV calling from fermikit ?
- "seqtk mergepe" is correct for multiple Lane fq DATA ?
- Please add a license HOT 2
- Can it call variants on tetraploid species?
- Error in make HOT 1
- GFA output? HOT 6
- Error in running fermikit
- make: nothing to be done for all
- (ha)ploidy HOT 7
- fermikit-0.12.tar.bz2 has weird Mac OS extensions HOT 2
- pipeline questions HOT 3
- joint calling HOT 5
- Error in last command of run-calling HOT 4
- High RAM usage on simulated samples HOT 1
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from fermikit.