Bioconductor Release 3.16

CHANGES IN VERSION 1.38.0

UTILITIES

• new option 'ext_nbyte' in seqGet2bGeno()
• seqAlleleCount() and seqGetAF_AC_Missing() return NA instead of zero when all genotypes are missing at a site
• seqGDS2VCF() does not output the FORMAT column if there is no selected sample (e.g., site-only VCF files)
• seqGetData(, "$chrom_pos2") is similar to seqGetData(, "$chrom_pos") except the duplicates with the suffix ("_1", "_2" or >2)

NEW FEATURES

• seqGDS2BED() can convert to PLINK BED files with the best-guess genotypes when there are only numeric dosages in the GDS file
• seqEmptyFile() outputs an empty GDS file