Missing/incorrect columns in SNV/indel final output files

[kanika-arora]

Description of the bug

SNV/indel final file is missing

• HGVSp_Short
• a column to indicate whether the variant is clinically signed out or not

The following columns are incorrect and should be replaced

• the name t_alt_count doesn't make sense since the rows have both tumors and normals -> replace with alt_count
• the name t_total_count doesn't make sense since the rows have both tumors and normals -> replace with total_count
• Tumor_Seq_Allele2 doesn't make sense since the rows have both tumors and normals -> replace with something like Alternate_Allele
• Try be consistent with names across columns - i.e. all in title case or all in lower case.

The current script makes it very difficult to see which columns are being used for the allele counts.

• Add comments and help text in the beginning of the filter script to specify which allele counts are being used for which file type.

Command used and terminal output

Relevant files

No response

System information

No response

[kanika-arora]

Other issues:

• There is "-ORG-STD" in some of the sample names in sample_id of the final SNV/INDEL file
• The read_type is "ORG-STD" for some? Should be "standard" and/or "unfiltered"
• clonality, tcn,expected_alt_copies, is NA for some and blank for other rows when not present