Filtered and selected data .zip files

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Exporting filtered or selected data creates a .zip file that contains five .csv files and a ReadMe.txt file. 

AF.csv

This file contains the allele frequency broken down by sample per subclone and cell for each variant. The frequency is calculated as the number of reads with evidence for a mutation out of the total number of reads times 100.

DP.csv

This file contains the read depth broken down by sample per subclone and cell for each variant. The read depth per variant metric is the filtered depth at the cell level. This provides the number of filtered reads that support each of the reported alleles.

GQ.csv

This file contains the genotype quality score broken down by sample per subclone and cell for each variant. The genotype quality score represents the Phred-scaled confidence that the genotype assignment (GT) is correct, derived from the genotype normalized likelihoods of possible genotypes (PL). Refer to this section for more information.

NGT.csv

This file contains the genotype call converted to categorical values broken down by sample per subclone and cell for each variant.

The values represent:

0 – Reference

1 – Heterozygous mutation

2 – Homozygous mutation

3 – Unknown

The calls are made by GATK/HaplotypeCaller.

ReadMe.txt

This file explains the .csv files contained in the .zip file.

Variants.csv

This file contains the variant metadata.

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