command line

parse_lc_bas.pl -summary 20140502_complete_sample_summary.txt -lc_bas 20130502.low_coverage.alignment.index.bas.gz -e_bas 20130502.exome.alignment.index.bas.gz -e_hsmetrics 20130502.exome.alignment.index.HsMetrics.gz -cg_index 20130820.cg_data.index -pcr_free 20140502.high_coverage_pcr_bams -broad_omni Omni25_genotypes_2141_samples.b37.v2.vcf.gz -sanger_omni ALL.wgs.sanger_omni_2_5_8.20130805.snps.chip.genotypes.vcf.gz -coriell_affy ALL.wgs.nhgri_coriell_affy_6.20131213.snps_indels.chip.genotypes.vcf.gz -axiom Affymetrix_Axiom_DB_2010_v4_b37.vcf.gz -broad_exome ALL.wex.broad_lof_exome_chip_beadstudio.20130703.snps_and_indels.chip.genotypes.vcf.gz -pedigree 20140502_all_samples.ped

Source of files

20140502_complete_sample_summary.txt 

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140502_sample_summary_info/20140502_complete_sample_summary.txt

20130502.low_coverage.alignment.index.bas.gz 

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices/20130502.low_coverage.alignment.index.bas.gz

20130502.exome.alignment.index.bas.gz 

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices/20130502.exome.alignment.index.bas.gz

20130502.exome.alignment.index.HsMetrics.gz 

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices/20130502.exome.alignment.index.HsMetrics.gz

20130820.cg_data.index 

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/complete_genomics_indices/20130820.cg_data.index

20140502.high_coverage_pcr_bams 

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140502_sample_summary_info/20140502.high_coverage_pcr_bams

Omni25_genotypes_2141_samples.b37.v2.vcf.gz 

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20131122_broad_omni/Omni25_genotypes_2141_samples.b37.v2.vcf.gz

ALL.wgs.sanger_omni_2_5_8.20130805.snps.chip.genotypes.vcf.gz  

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130812_sanger_omni/ALL.wgs.sanger_omni_2_5_8.20130805.snps.chip.genotypes.vcf.gz

ALL.wgs.nhgri_coriell_affy_6.20131213.snps_indels.chip.genotypes.vcf.gz 

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20131122_coriell_affy6/ALL.wgs.nhgri_coriell_affy_6.20131213.snps_indels.chip.genotypes.vcf.gz

Affymetrix_Axiom_DB_2010_v4_b37.vcf.gz

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110210_Affymetrix_Axiom/Affymetrix_Axiom_DB_2010_v4_b37.vcf.gz

ALL.wex.broad_lof_exome_chip_beadstudio.20130703.snps_and_indels.chip.genotypes.vcf.gz 

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20130703_broad_lof_exome_chip/ALL.wex.broad_lof_exome_chip_beadstudio.20130703.snps_and_indels.chip.genotypes.vcf.gz

20140502_all_samples.ped

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140502_sample_summary_info/20140502_all_samples.ped