Genomecomb moved to github on https://github.com/derijkp/genomecomb
with documentation on https://derijkp.github.io/genomecomb.
For up to date versions, go there. These pages only remain here for the data on the older scientific
application (or if someone really needs a long obsolete version of the software)
samtools based variant file
Variant files created by genomecomb using the samtools variant
caller are in the usual genomecomb tab-separated variant file format
(tsv). besides the usual fields of a variant
tsv file, they (can) also contain the following columns:
- totalcoverage
- Raw read depth (DP in vcf INFO); samtools does not count all
mapping reads for totalcoverage (bad reads are filtered out)
- coverage
- number of high-quality bases (DP in vcf FORMAT); bases with
quality < 13 are filtered out as well
- genoqual
- genotype quality, encoded as a phred quality
-10log_10p(genotype call is wrong)
- phased
- 1 if genotype is phased, 0 otherwise
- genotypes
- list of allele numbers (0 for ref, 1 for first alt, ...) (GT
in vcf) The alleles are comma (,) separated for phased genotypes (|
in vcf), and ";" separated for unphased (/ in vcf). In
contrast to alleleSeq1 and alleleSe2, this field allows for
ploidies other than 2
- loglikelihood
- Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)
- DV
- number of high-quality non-reference bases
- SP
- Phred-scaled strand bias P-value
- PL
- List of Phred-scaled genotype likelihoods
- DP4
- number of high-quality ref-forward bases, ref-reverse,
alt-forward and alt-reverse bases
- MQ
- Root-mean-square mapping quality of covering reads
- FQ
- Phred probability of all samples being the same
- AF1
- Max-likelihood estimate of the first ALT allele frequency
(assuming HWE)
- AC1
- Max-likelihood estimate of the first ALT allele count (no HWE
assumption)
- totalallelecount
- Total number of alleles in called genotypes
- IS
- Maximum number of reads supporting an indel and fraction of
indel reads
- allelecount
- Allele count in genotypes for each ALT allele, in the same
order as listed
- G3
- ML estimate of genotype frequencies
- HWE
- Chi^2 based HWE test P-value based on G3
- CLR
- Log ratio of genotype likelihoods with and without the
constraint
- UGT
- The most probable constrained genotype configuration in the
trio
- CGT
- P-values for strand bias, baseQ bias, mapQ bias and tail
distance bias
- PV4
- P-values for strand bias, baseQ bias, mapQ bias and tail
distance bias
- INDEL
- Indicates that the variant is an INDEL.
- PC2
- Phred probability of the nonRef allele frequency in group1
samples being larger (,smaller) than in group2.
- PCHI2
- Posterior weighted chi^2 P-value for testing the association
between group1 and group2 samples.
- QCHI2
- Phred scaled PCHI2
- PR
- number of permutations yielding a smaller PCHI2.
- QBD
- Quality by Depth: QUAL/#reads
- RPB
- Read Position Bias
- MDV
- Maximum number of high-quality nonRef reads in samples
- VDB
- Variant Distance Bias (v2) for filtering splice-site
artefacts in RNA-seq data. Note: this version may be broken.
- cluster
- variant is in a region containing many closeby variant calls
