misc.

download_human_fasta.sh

# GRCh37.p13
# $ wget -r ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/Primary_Assembly/assembled_chromosomes/FASTA/
# $ for x in {1..22} X Y; do gzip -dc chr${x}.fa.gz >> GRCh37.p13.fa; done

# UCSC hg18 (Build36.1)  -- http://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/
# $ wget -r -l1 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/'
# $ for x in {1..22} X Y; do gzip -dc hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes/chr${x}.fa.gz >> hg18.fa; done

# UCSC hg17 (Build35)  -- http://hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/
# $ wget -r -l1 'ftp://hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/'
# $ for x in {1..22} X Y; do gzip -dc hgdownload.cse.ucsc.edu/goldenPath/hg17/chromosomes/chr${x}.fa.gz >> hg17.fa; done

$ cat hg19_rCRS.region.bed
chrM    0       16569
chr1    0       249250621
chr2    0       243199373
chr3    0       198022430
chr4    0       191154276
chr5    0       180915260
chr6    0       171115067
chr7    0       159138663
chr8    0       146364022
chr9    0       141213431
chr10   0       135534747
chr11   0       135006516
chr12   0       133851895
chr13   0       115169878
chr14   0       107349540
chr15   0       102531392
chr16   0       90354753
chr17   0       81195210
chr18   0       78077248
chr19   0       59128983
chr20   0       63025520
chr21   0       48129895
chr22   0       51304566
chrX    0       155270560
chrY    0       59373566

$ gzip -dc genome.gvcf.gz| break_blocks --region-file hg19_rCRS.region.bed --ref hg19_rCRS.fa| bgzip -c > genome.vcf.bgz

$ tabix -p vcf file.vcf.bgz