A new GATK came out and now does indel calling, which was lacking before I think. Its web page is one of the worst to me, since it is hard to find things in it.
But it has one of the best supporting discussion group: a lot of things to learn in there. Pitifully, its VCF does not describe type of indels. So users must classify them. They must change this.
##FILTER=<ID=LowQual,Description=”Low quality”>
##FORMAT=<id=ad,number=.,type=integer,description=”allelic depths=”” for=”” the=”” ref=”” and=”” alt=”” alleles=”” <span=”” class=”hiddenSpellError” pre=”alleles “>in the order listed”>
##FORMAT=<ID=DP,Number=1,Type=Integer,Description=”Approximate read depth (reads with MQ=255 or with bad mates are filtered)”>
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=”Genotype Quality”>
##FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”>
##FORMAT=<id=pl,number=g,type=integer,description=”normalized, <span=”” class=”hiddenSpellError” pre=””>Phred-scaled likelihoods for genotypes as defined in the VCF specification”>
##INFO=<ID=AC,Number=A,Type=Integer,Description=”Allele count in genotypes, for each ALT allele, in the same order as listed”>
##INFO=<ID=AF,Number=A,Type=Float,Description=”Allele Frequency, for each ALT allele, in the same order as listed”>
##INFO=<ID=AN,Number=1,Type=Integer,Description=”Total number of alleles in called genotypes”>
##INFO=<id=baseqranksum,number=1,type=float,description=”z-score from=”” <span=”” class=”hiddenSpellError” pre=”from “>Wilcoxon rank sum test of Alt Vs. Ref base qualities”>
##INFO=<id=dp,number=1,type=integer,description=”approximate read=”” depth;=”” some=”” <span=”” class=”hiddenSpellError” pre=”some “>reads may have been filtered”>
##INFO=<ID=DS,Number=0,Type=Flag,Description=”Were any of the samples downsampled?”>
##INFO=<ID=Dels,Number=1,Type=Float,Description=”Fraction of Reads Containing Spanning Deletions”>
##INFO=<ID=FS,Number=1,Type=Float,Description=”Phred-scaled p-value using Fisher’s exact test to detect strand bias”>
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description=”Consistency of the site with at most two segregating haplotypes”>
##INFO=<id=inbreedingcoeff,number=1,type=float,description=”inbreeding coefficient=”” as=”” estimated=”” from=”” the=”” genotype=”” <span=”” class=”hiddenSpellError” pre=”genotype “>likelihoods per-sample when compared against the Hardy-Weinberg expectation”>
##INFO=<id=mleac,number=a,type=integer,description=”maximum likelihood=”” expectation=”” (<span=”” class=”hiddenSpellError” pre=””>MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed”>
##INFO=<id=mleaf,number=a,type=float,description=”maximum likelihood=”” expectation=”” (<span=”” class=”hiddenSpellError” pre=””>MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed”>
##INFO=<ID=MQ,Number=1,Type=Float,Description=”RMS Mapping Quality”>
##INFO=<ID=MQ0,Number=1,Type=Integer,Description=”Total Mapping Quality Zero Reads”>
##INFO=<id=mqranksum,number=1,type=float,description=”z-score from=”” <span=”” class=”hiddenSpellError” pre=”From “>Wilcoxon rank sum test of Alt vs. Ref read mapping qualities”>
##INFO=<ID=QD,Number=1,Type=Float,Description=”Variant Confidence/Quality by Depth”>
##INFO=<ID=RPA,Number=.,Type=Integer,Description=”Number of times tandem repeat unit is repeated, for each allele (including reference)”>
##INFO=<id=ru,number=1,type=string,description=”tandem repeat=”” unit=”” (<span=”” class=”hiddenSpellError” pre=””>bases)”>
##INFO=<id=readposranksum,number=1,type=float,description=”z-score from=”” <span=”” class=”hiddenSpellError” pre=”from “>Wilcoxon rank sum test of Alt vs. Ref read position bias”>
##INFO=<ID=SB,Number=1,Type=Float,Description=”Strand Bias”>
##INFO=<ID=STR,Number=0,Type=Flag,Description=”Variant is a short tandem repeat”>
51.220581
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