A computer-implemented method for germline variant calling, the method comprising: obtaining a reference sequence, a plurality of sequence reads, and a position of a candidate variant within the sequence reads; obtaining augmented sequence reads by inserting one or more spaces in one or more sequence reads; obtaining an augmented reference sequence by inserting one or more spaces in the reference sequence; converting a segment of the augmented sequence reads around the candidate variant into a sample matrix; converting a segment of the augmented reference sequence around the candidate variant into a reference matrix, wherein the sample matrix comprises: at least four lines representing four types of nucleotide bases, each line representing the number of bases of the respective nucleotide base type at different positions within the segment of the augmented sequence reads; and at least one line representing the number of inserted spaces at different positions within the segment of the augmented sequence reads; providing the sample matrix and the reference matrix to a trained neural network; and obtaining, at the output of the trained neural network, prediction data related to a variant within the plurality of sequence reads,wherein the prediction data related to the variant comprises at least one of: a predicted type of the variant; a predicted position of the variant; a predicted length of the variant; and a predicted genotype of the variant, the method further comprising: detecting one or more inserted bases within the plurality of sequence reads, wherein augmenting the sequence reads and the reference sequence comprises: for each inserted base detected in any of the sequence reads, inserting a space in the reference sample at the position of the inserted base; and for each inserted base detected in any of the sequence reads, inserting a space at the position of the inserted base in every sequence read for which no insertions were detected at the position of the inserted base. obtaining a reference sequence, a plurality of sequence reads, and a position of a candidate variant within the sequence reads; obtaining augmented sequence reads by inserting one or more spaces in one or more sequence reads; obtaining an augmented reference sequence by inserting one or more spaces in the reference sequence; converting a segment of the augmented sequence reads around the candidate variant into a sample matrix; converting a segment of the augmented reference sequence around the candidate variant into a reference matrix, wherein the sample matrix comprises: at least four lines representing four types of nucleotide bases, each line representing the number of bases of the respective nucleotide base type at different positions within the segment of the augmented sequence reads; and at least one line representing the number of inserted spaces at different positions within the segment of the augmented sequence reads; at least four lines representing four types of nucleotide bases, each line representing the number of bases of the respective nucleotide base type at different positions within the segment of the augmented sequence reads; and at least one line representing the number of inserted spaces at different positions within the segment of the augmented sequence reads; providing the sample matrix and the reference matrix to a trained neural network; and obtaining, at the output of the trained neural network, prediction data related to a variant within the plurality of sequence reads,wherein the prediction data related to the variant comprises at least one of: a predicted type of the variant; a predicted position of the variant; a predicted length of the variant; and a predicted genotype of the variant, the method further comprising: a predicted type of the variant; a predicted position of the variant; a predicted length of the variant; and a predicted genotype of the variant, the method further comprising: detecting one or more inserted bases within the plurality of sequence reads, wherein augmenting the sequence reads and the reference sequence comprises: for each inserted base detected in any of the sequence reads, inserting a space in the reference sample at the position of the inserted base; and for each inserted base detected in any of the sequence reads, inserting a space at the position of the inserted base in every sequence read for which no insertions were detected at the position of the inserted base. for each inserted base detected in any of the sequence reads, inserting a space in the reference sample at the position of the inserted base; and for each inserted base detected in any of the sequence reads, inserting a space at the position of the inserted base in every sequence read for which no insertions were detected at the position of the inserted base.