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I believe you may be able to map your reads, but I don't know how to do that with minimap2. I recommend running gsnap, which is more SNP tolerant and provides a number of parameters which are likely to help. For instance, I believe that most aligners will treat 'N' characters as mismatches when you align. GSNAP has parameters to account for this. --...

3

According to the VCF specification, haplotype blocks are defined by the "Phase Set" [PS] tag: PS : phase set. A phase set is defined as a set of phased genotypes to which this genotype belongs. Phased genotypes for an individual that are on the same chromosome and have the same PS value are in the same phased set. A phase set specifies multi-marker ...

3

Assuming your files are as you show, and the genotype field is always the 1st entry of the sample information field (the 10th), then you can just do this directly with a simple awk script: $awk -F"\t" -vOFS="\t" 'BEGIN{print "#CHROM","POS","ID","REF","ALT","Truth","Test"}{ if(/^[^#]/){var=$1$2$4$5; gt=substr($10,1,3); if(NR==FNR){a[var]=gt; next;} if(var ...

2

For simple haplotype simulation of unrelated individuals, there is Montana's venerable HapSim. The model used in that tool is simple and may be good enough for your purposes. You will need to acquire a recombination rate map from for example the HapMap consortium or from 1000G. A cursory google search also revealed this tool and walkthrough that may be ...

2

The data in your matrix appears to be from a VCF file (For reference, see https://github.com/samtools/hts-specs/blob/master/VCFv4.3.pdf). In the VCF specification, a heterozygous genotype can be specified as 0|1. The zero and one indicate the allele numbers (0=ref, 1=first alt) that make up the genotype. The "pipe" (|) is used to indicate that the alleles ...

2

The HapMap website was suspended due to a security issue. Archived HapMap data is available via FTP, but it's a better idea to download up-to-date International Genome data from the IGSR website (which includes the HapMap individuals as a subset). The format you use will be dependent on the data analysis program you're using. In most cases involving SNP ...

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Phasing means that you are able to distinguish the both copies of your target sequence. (Usually you have one from your mother and one from your father). If you can do this, depends mainly on the sequencing technology you are using. For example in case of sanger sequencing, you cannot do this, because you (pre)amplify all your copies at once and detect the ...

1

It depends on the scale of the data (i.e. number of individuals, number of SNPs). Generally this can be done by matching up individual SNP genotypes to haplotype tag SNPs. The specific combination of genotyped SNPs is used to determine the underlying haplotype, based on tag SNP frequencies for each haplotype. More details of the process of identifying tag ...

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Yes, your question makes alot of sense and its a good question because hits at the heart of differences between population genetic analysis and phylogenetic analysis. However, when you speak about gaps you are referring to 'indels' (insertion/deletion). Indels The conservative approach is to simply delete sites with gaps. Arlequin uses a lot of maximum ...

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Many (small) variant calling algorithms use pileups to genotype variants position-by-position. This approach alone is insufficient to phase adjacent variants. However, if the variants of interest are close enough to be covered by a single read, it's certainly possible to phase them even with <100bp Illumina reads. In fact, I was implementing just such an ...

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Two options that immediately come to mind, depending on what you hope to accomplish down the pipeline: you might simply mark the unphased sites with a "/" instead of "|" to indicate they are not phased; or, if you have multiple haplotype blocks that are all independent of each other, you could use the chromosome field to identify each unique haplotype (e.g. ...

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This is a haplotype map, where each node is proportional to the frequency of a given allele. The formal tool to do this is Network 5 found here. The problem with manaul haplotype maps is the area of the node should be proportional to the frequency, if this is not accurate it could be perceived to be misleading. The approach for looking at each parsimonious ...

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I am not sure I understood all, but what you do is like doing a Markov chain but instead of saying that the previous position(s) decides the fate of the next one(s) is the block what determines which other block follows it. Mathematically I think that could be explained in terms of linkage disequilibrium (and wikipedia page), but instead of using a single ...

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There is a new idea of reporting the "phased haplotype/genotype block" with unique block ID. phaser uses "PI" (unique phase-index) and "PG" (phased-genotype). GATK is also using this idea of "unique-block" and "phased-genotype"; See the "HP" tag. Personally, I feel the representation of "phaser" is way better and comprehensive. I would represent your ...

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