Created
February 28, 2020 20:33
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Download and clean up dependent data for lab 7 (HG471 @ UChicago)
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| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/hapmap_3.3.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_omni2.5.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_omni2.5.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase3_v4_20130502.sites.vcf.gz.md5 | |
| wget ftp://ftp.1000genomes.ebi.ac.uk//vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz |
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| module load samtools | |
| module load picard | |
| zcat hs37d5.fa.gz|head -n 48017254|tail -n 855078 > hs37d5_chr22.fa | |
| samtools faidx hs37d5_chr22.fa | |
| java -jar $PICARD CreateSequenceDictionary REFERENCE=hs37d5_chr22.fa OUTPUT=hs37d5_chr22.dict | |
| module load htslib | |
| unzipVCF () { | |
| filename=$1 | |
| echo Processing $filename | |
| zcat /project2/hgen47100/data/lab7/$filename.gz > /project2/hgen47100/data/lab7/$filename | |
| # tabix vcf /project2/hgen47100/data/lab7/$filename | |
| # mv /project2/hgen47100/data/lab7/$filename.tmp /project2/hgen47100/data/lab7/$filename | |
| # mv /project2/hgen47100/data/lab7/$filename.tmp.tbi /project2/hgen47100/data/lab7/$filename.tbi | |
| } | |
| unzipVCF "hapmap_3.3.b37.vcf" | |
| unzipVCF "1000G_omni2.5.b37.vcf" | |
| unzipVCF "1000G_phase1.snps.high_confidence.b37.vcf" | |
| unzipVCF "dbsnp_138.b37.vcf" |
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