Data Slicer

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This tool will get a subset of data from a BAM or VCF file.

Name for this job (optional):

Species:

Human

Assembly: GRCh37.p13

Choose file format:

Region Lookup:

e.g. 1:1-50000

Choose data collections or provide your own file URLs:

Genotype File URL:

Sample-population file URL: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panelSample-population file URL: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/phase1_integrated_calls.20101123.ALL.panelSample-population file URL: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_male_samples_v3.20130502.ALL.panel

The genotype file should be VCF only.<a href="/info/website/upload/sample_files/Pulmonary_function.vcf.txt" class="popup"> Example VCF file </a>Genotype file URL:

e.g: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz

Choose whether to apply any filtering to the output.Filters:

No filtering

By individuals

By populations

This file lists all the individuals and the population they come from.<a href="/info/docs/tools/allelefrequency/sample_panel.html" class="popup">Find out more on what a panel file is.</a>Sample-population mapping file URL:

e.g: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel

Select one or more phase 3 populations:

Select one or more phase 1 populations:

Select one or more phase 3(male) populations:

Select one or more populations:

Enter comma separated list of individuals:

maximum 372 individuals

Alternatively, select one or more individuals from the scrollable list:

maximum 416 individuals

BAM file URL:

e.g: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/data/NA06984/alignment/NA06984.454.MOSAIK.SRP000033.2009_11.bam

Generate .bai file:

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ACB
ASW
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CDX
CEU
CHB
CHS
CLM
ESN
FIN
GBR
GIH
GWD
IBS
ITU
JPT
KHV
LWK
MSL
MXL
PEL
PJL
PUR
STU
TSI
YRI

ACB
ASW
BEB
CDX
CEU
CHB
CHS
CLM
ESN
FIN
GBR
GIH
GWD
IBS
ITU
JPT
KHV
LWK
MSL
MXL
PEL
PJL
PUR
STU
TSI
YRI

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