fix: use correct bcftools filter column for tumor in manta tumor only

[mathiasbio]

This PR:

Correct bcftools filter in tumor / normal Manta rule to use the tumor column instead of the normal (bug).

Issue was discovered during validation that the bcftools filter in the manta_tumor_normal rule was using the normal column for filtering (index 0) instead of the tumor (index 1). This is not an issue in the manta_tumor_only as the tumor there is index 0. By switching the sample in the tumor_normal manta rule to index 1 for the filter, it should work as expected.

Fixed: for any bug fixes.

• switched to use column 2 in the bcftools filter for the low_prsr filter in manta_tumor_normal rule

Tests to verify that issue is correct:

Run bcftools on the raw somantic manta calls on tumor-normal cases and confirm that it applies filter on tumor column in sample: K (see https://docs.google.com/document/d/12x3ozQE62bk_yWNTBW_u8vZMqhpKFRMW3yizzM_mWZs/)

command: bcftools filter --threads 2 --exclude 'SUM(FORMAT/PR[1:1]+FORMAT/SR[1:1]) < 4' --soft-filter 'newfilter' --mode '+'

Sets filter on 5 variants: PR:SR 66,0:82,0 (normal) 31,1:38,2 (tumor)

original command sets filter on 504 variants: PR:SR 52,0:61,0 (normal) 63,5:81,2 (tumor)

• Filter is working correctly!

Review and tests:

• Tests pass
• Code review
• New code is executed and covered by tests, and test approve

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (410dd9e) 99.44% compared to head (330f0fa) 99.44%.

Additional details and impacted files

@@               Coverage Diff                @@
##           release_v14.0.0    #1400   +/-   ##
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  Coverage            99.44%   99.44%           
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  Files                   40       40           
  Lines                 1983     1983           
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  Hits                  1972     1972           
  Misses                  11       11           

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unittests	99.44% <ø> (ø)

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[sonarqubecloud]

Quality Gate passed

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[ivadym]

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