Test data replacement addition chart

Test data replacement/addition chart

New File Name:	Source File Name:	Replacing file:	description:	repo-location	Source File origin:
Germline:
test2.recal	test.recal	New File	Recalibration table output from VariantRecalibrator, used by ApplyVQSR	data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/	https://github.com/GCJMackenzie/test_data/tree/master/vrecals_base
test2.recal.idx	test.recal.idx	New File	Recalibration table index output from VariantRecalibrator, used by ApplyVQSR	data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/	https://github.com/GCJMackenzie/test_data/tree/master/vrecals_base
test2.tranches	test.tranches	New File	Recalibration table tranches output from VariantRecalibrator, used by ApplyVQSR	data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/	https://github.com/GCJMackenzie/test_data/tree/master/vrecals_base
test2_allele_specific.recal	test_allele_specific.recal	New File	Allele specific Recalibration table output from VariantRecalibrator, used by ApplyVQSR	data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/	https://github.com/GCJMackenzie/test_data/blob/master/vrecals_as/
test2_allele_specific.recal.idx	test_allele_specific.recal.idx	New File	Allele specific Recalibration table index output from VariantRecalibrator, used by ApplyVQSR	data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/	https://github.com/GCJMackenzie/test_data/blob/master/vrecals_as/
test2_allele_specific.tranches	test_allele_specific.tranches	New File	Allele specific Recalibration table tranches output from VariantRecalibrator, used by ApplyVQSR	data/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/	https://github.com/GCJMackenzie/test_data/blob/master/vrecals_as/
test2_germline_1.fq.gz	normal_0.000+disease_1.000_1.fq.gz	New File	Synthetic raw reads file used to generate disease test data for HaplotypeCaller	data/genomics/homo_sapiens/illumina/fastq/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/
test2_germline_2.fq.gz	normal_0.000+disease_1.000_2.fq.gz	New File	Synthetic raw reads file used to generate disease test data for HaplotypeCaller	data/genomics/homo_sapiens/illumina/fastq/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/
test_germline_1.fq.gz	normal_1.000+disease_0.000_1.fq.gz	New File	Synthetic raw reads file used to generate normal test data for HaplotypeCaller	data/genomics/homo_sapiens/illumina/fastq/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/
test_germline_2.fq.gz	normal_1.000+disease_0.000_2.fq.gz	New File	Synthetic raw reads file used to generate normal test data for HaplotypeCaller	data/genomics/homo_sapiens/illumina/fastq/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/reads/
test2_haplotc.vcf.gz	HaplotypeCaller_disease_103.vcf.gz	New File	vcf output from HaplotypeCaller using germline disease reads	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test2_haplotc.vcf.gz.tbi	HaplotypeCaller_disease_103.vcf.gz.tbi	New File	vcf.tbi output from HaplotypeCaller using germline disease reads	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test_haplotc.vcf.gz	HaplotypeCaller_normal.vcf.gz	New File	vcf output from HaplotypeCaller using germline normal reads	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test_haplotc.vcf.gz.tbi	HaplotypeCaller_normal.vcf.gz.tbi	New File	vcf.tbi output from HaplotypeCaller using germline normal reads	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test2_haplotc_snpeff.ann.vcf.gz	HaplotypeCaller_disease_103_snpEff.ann.vcf.gz	New File	vcf output from HaplotypeCaller using germline disease reads annotated using snpEff	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test2_haplotc_snpeff.ann.vcf.gz.tbi	HaplotypeCaller_disease_103_snpEff.ann.vcf.gz.tbi	New File	vcf.tbi output from HaplotypeCaller using germline disease reads annotated using snpEff	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test_haplotc_snpeff.ann.vcf.gz	HaplotypeCaller_normal_snpEff.ann.vcf.gz	New File	vcf output from HaplotypeCaller using germline normal reads annotated using snpEff	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
test_haplotc_snpeff.ann.vcf.gz.tbi	HaplotypeCaller_normal_snpEff.ann.vcf.gz.tbi	New File	vcf.tbi output from HaplotypeCaller using germline normal reads annotated using snpEff	data/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/	https://github.com/lescai-teaching/datasets_class/tree/master/germline_calling/variants
Somatic:
New File Name:	tumour.recal.bam	Replacing file:	description:	repo-location	Source File origin:
New File Name:	normal.recal.bam	Replacing file:	description:	repo-location	Source File origin:
New File Name:	tumour.recal.bam.bai	Replacing file:	description:	repo-location	Source File origin:
New File Name:	tumour.recal.bam.bai	Replacing file:	description:	repo-location	Source File origin:
Reference: