Index

Annotate

Custom annotation

Calculate Statistics

Define cohorts

Remove

Import

Export

Export statistics

Export statistics is an special case of export. Instead of export full variants, only the variant cohort statistics are exported.

As for variants export, there are multiple possible output formats:

TSV (Tab Separated Values). Simple format with each cohort in one column.

#CHR    POS    REF    ALT    ALL_AN    ALL_AC    ALL_AF    ALL_HET    ALL_HOM
22    16050213    C    T    1000    1    0.001    0.002    0.0
22    16050607    G    A    1000    2    0.002    0.004    0.0
22    16050740    A    -    1000    1    0.001    0.002    0.0
22    16050840    C    G    1000    13    0.013    0.026    0.0
22    16051075    G    A    1000    2    0.002    0.004    0.0
22    16051249    T    C    1000    91    0.091    0.162    0.01
22    16051453    A    C    998    74    0.074    0.144    0.004
22    16051453    A    G    926    2    0.002    0.144    0.004
22    16051723    A    -    1000    12    0.012    0.024    0.0
22    16051816    T    G    1000    2    0.002    0.004    0.0

Operations

Variant Storage Operations are responsible for leaving variant data ready for querying and analysis, for instance VCF loading, integrity checks, sample genotype aggregation, indexing, or variant annotation are examples of operations. Operations can only be executed by admin users. Many operations write and update indexed data, this will significantly improve the quality and performance of different queries and analysis.

The OpenCGA Variant Storage Engine supports several operations to work with variant datasets:

• Sample Genotype Aggregation
• Variant Annotation
• Secondary Index
• Export / Import

Index Pipeline

Image Added