Yes, they have non-overlapping variants, that will be singletons and which we definitely want to preserve.
In terms of info field, my main interest is combining into a single VCF to be able to do variant QC, so I’d like to maintain the GQ, DP - but I think that’s calculated from the entries right?
Here is the description of one sample specific VCF
Global fields:
** None**
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Column fields:
** ‘s’: str**
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Row fields:
** ‘locus’: locus**
** ‘alleles’: array**
** ‘rsid’: str**
** ‘qual’: float64**
** ‘filters’: set**
** ‘info’: struct {**
** AC: array, **
** AF: array, **
** AN: int32, **
** BaseQRankSum: float64, **
** ClippingRankSum: float64, **
** DP: int32, **
** DS: bool, **
** END: int32, **
** ExcessHet: float64, **
** FS: float64, **
** HaplotypeScore: float64, **
** InbreedingCoeff: float64, **
** MLEAC: array, **
** MLEAF: array, **
** MQ: float64, **
** MQ0: int32, **
** MQRankSum: float64, **
** NEGATIVE_TRAIN_SITE: bool, **
** POSITIVE_TRAIN_SITE: bool, **
** QD: float64, **
** RAW_MQ: float64, **
** ReadPosRankSum: float64, **
** SOR: float64, **
** VQSLOD: float64, **
** VariantType: str, **
** culprit: str**
** }**
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Entry fields:
** ‘AB’: float64**
** ‘AD’: array**
** ‘DP’: int32**
** ‘GQ’: int32**
** ‘GT’: call**
** ‘MIN_DP’: int32**
** ‘MQ0’: int32**
** ‘PGT’: call**
** ‘PID’: str**
** ‘PL’: array**
** ‘RGQ’: int32**
** ‘SB’: array**
----------------------------------------
Column key: [‘s’]
Row key: [‘locus’, ‘alleles’]
----------------------------------------