DIFFERENTIATION OF COINFECTION FROM CONTAMINATION WITHIN GENETIC SAMPLES

1 . A method of distinguishing between coinfection and contamination for a biological sample, the biological sample including a first variant of a pathogen and a second variant of the pathogen, wherein the first variant corresponds to a first mutation and the second variant corresponds to a second mutation different than the first mutation, the method comprising:

acquiring sequencing data for the biological sample, the sequencing data including a plurality of reads;

determining that the biological sample is a mixed sample of the first variant and the second variant based on an alternative allele fraction calculated according to the plurality of reads;

searching individual reads of the plurality of reads for recombinant reads that include the first mutation and the second mutation; and

determining whether the biological sample is indicative of a coinfection or a contamination, based on an amount of the recombinant reads that each indicate both the first variant and the second variant.

2 . The method of claim 1 , wherein determining that the biological sample is a mixed sample comprises calling an alternative allele at a locus based on either the first mutation or the second mutation.

3 . The method of claim 2 , wherein determining that the biological sample is a mixed sample comprises calculating an alternative allele fraction for the called alternative allele.

4 . The method of claim 3 , wherein calculating an alternative allele fraction for one of the called alternative alleles is based on a number of reads of the called alternative allele divided by a total number of reads at the locus.

5 . The method of claim 1 , further comprising selecting the first variant and the second variant of the pathogen, wherein selecting the first variant and the second variant comprises retrieving information from a database.

6 . The method of claim 1 , wherein determining that the biological sample is a mixed sample comprises calculating at least one of a median alternative allele fraction, a mean alternative allele fraction, a weighted alternative allele fraction, or an average alternative allele fraction, based on one or more calculated alternative allele fractions.

7 . The method of claim 6 , wherein calculating at least one of a median alternative allele fraction, a mean alternative allele fraction, a weighted alternative allele fraction, or an average alternative allele fraction is based on loci that have alternative allele fractions of at least a threshold minimum fraction.

8 . The method of claim 7 , wherein the threshold minimum fraction is about 0.15.

9 . The method of claim 7 , wherein if the calculation based on the alternative allele fraction is below a threshold alternative allele fraction, the sample is a mixed sample.

10 . The method of claim 7 , wherein if the calculation based on the alternative allele fraction is above a threshold alternative allele fraction, the sample is dominant in one of the first variant and the second variant.

11 . The method of claim 10 , wherein the threshold alternative allele fraction is about 0.80.

12 . The method of claim 1 , wherein detecting a recombinant pathogen comprises identifying reads or read pairs straddling at least one of the first mutation and the second mutation.

13 . The method of claim 1 , wherein determining whether the biological sample is indicative of a coinfection or a contamination comprises walking across the sequence from a 5′ end to a 3′ end to determine whether the first mutation, the second mutation, or combinations thereof are present.

14 . The method of claim 1 , wherein determining whether the biological sample is indicative of a coinfection or a contamination comprises identifying reads that start with the first mutation and send with the second mutation.

15 . The method of claim 1 , wherein determining whether the biological sample is indicative of a coinfection or a contamination comprises identifying reads that include mutations from both the first variant and the second variant.

16 . The method of claim 1 , wherein determining whether the biological sample is indicative of a coinfection or a contamination comprises identifying one or more breakpoints.

17 . A non-transitory machine-readable medium including instructions that, when executed by a processor of a machine, cause the machine to perform operations comprising:

acquiring sequencing data for a biological sample, the sequencing data including a plurality of reads;

identifying a first variant and a second variant of the biological sample, the first variant corresponding to a first mutation and the second variant corresponding to a second mutation different than the first mutation;

determining that the biological sample is a mixed sample of the first variant and the second variant based on an alternative allele fraction calculated according to the plurality of reads;

searching individual reads of the plurality of reads for recombinant reads that include the first mutation and the second mutation; and

determining whether the biological sample is indicative of a coinfection or a contamination, based on an amount of the recombinant reads that each indicate both the first variant and the second variant.

18 . The non-transitory machine-readable medium of claim 17 , wherein determining whether the biological sample is a mixed sample comprises calling an alternative allele at a locus based on either the first mutation or the second mutation.

19 . The non-transitory machine-readable medium of claim 18 , wherein determining whether the biological sample is a mixed sample comprises calculating an alternative allele fraction for the called alternative allele.

20 . The non-transitory machine-readable medium of claim 19 , wherein calculating an allele fraction for one of the called alternative alleles comprises taking a number of reads of the called alternative allele divided by a total number of reads at the locus.