These VCF files were called on the full project BAM files derived from the
20101123 sequence.index files, using the glfMultiples/MaCH SNP caller, feeding
the BEAGLE haplotypes as starting point of MCMC procedure of MaCH.

A total of 1,004 individuals are subsetted into three continental population allowing overlaps - 563 Europeans, 475 Asians, and 387 Africans.

* All-population calls, subetted per continential population for LD-aware genotype refinement.
 - 20101123.chr20.michigan.filtered.AFR.{genotypes,sites}.vcf.gz
 - 20101123.chr20.michigan.filtered.ASN.{genotypes,sites}.vcf.gz
 - 20101123.chr20.michigan.filtered.EUR.{genotypes,sites}.vcf.gz

* ALL-population calls, softFiltered including the filtered out sites
 - 20101123.chr20.michigan.softFiltered.ALL.sites.vcf.gz
 
* Summary statistics of filtered call sets are as follows
------------------------------------------------------------------------
Callsets	#SNPs	#dbSNP	%dbSNP	Known	Novel	Overall	%HM3-re	
                    			Ts/Tv	Ts/Tv	Ts/Tv	discover
------------------------------------------------------------------------
AFR-PASS	578226	187460	32.4	2.33	2.36	2.35	98.318
ASN-PASS	476000	177957	37.4	2.33	2.36	2.35	97.331
EUR-PASS	542719	185735	34.2	2.33	2.36	2.35	98.258
------------------------------------------------------------------------
ALL-PASS	721250	190877	26.5	2.33	2.35	2.35	98.664
ALL-FAIL	94462	7770	8.2	1.47	1.04	1.07	0.254
ALL-TOTAL	815712	198647	24.4	2.29	2.08	2.12	98.918
------------------------------------------------------------------------

The following sets of filters are applied
* D[number] : Upper bound of total depth per site = 20x average
* d[number] : Lower bound of total depth per site = 0.5x average
* INDEL5 : SNPs located within 5-bp to 1KG pilot indels
* STR15 : Correlation coefficient of strand bias > 0.15
* str-15 : Correlation coefficient of strand bias < -0.15
* AB67 : Allele balance estimate > 0.67
* q5 : Lower bound of QUAL > 5