Isaac Turner
2014-10-01

1Mbp of chr22 from hg19 (GRCh37)

To generate:

    wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr22.fa.gz
    gzip -d chr22.fa.gz
    samtools faidx chr22.fa chr22:17000000-17999999 | tr -d 'n' | tr -d 'N' > chr22_17M_18M.fa

Check it is 1Mbp still

    dnacat -s chr22_17M_18M.fa

Index with BWA and samtools

    bwa index chr22_17M_18M.fa
    samtools faidx chr22_17M_18M.fa

