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Is it possible to use mapping.py with single-end reads or fasta sequences?

Hi,

I want to look at some clinical Candida parapsiolosis isolates because I want to make an NxN SNP matrix and MLT. I am use to looking at bacteria and came across this software. I've managed to install it but how do I run?

As a disclaimer Im not a bioinformatician I'm a microbiologist so self thought command line. Maybe its simple and I am missing sum thing but when I type "HaploTypo.py" to run the whole pipeline what other arguments do I have to put in? I have a reference .fna file but only as one file and not as --hapA and --hapB so I tried --ref with the -f1 and -f2 but it doesn't work and I tried running from the directory my fastq files are in thinking it might just work but it doesn't. I'm just wondering what I am missing and if someone could help? Id really appreciate it!

when I use -ref I get the error "unrecognized arguments"

Cheers,

P

Thanks for building such a useful pipeline! I'm happy to have found it, because it looks like it should work for exactly what I need.

I've been working on getting the pipeline working for me, but unfortunately have run into an error in the VCFcorr_alleles.py script that I believe is related to it having a hard time parsing my VCF files, but I haven't been able to figure out how to fix it myself. The error that I'm getting is:

Traceback (most recent call last):
  File "haplotypo/bin/3.5/VCFcorr_alleles.py.", line 391, in <module>
    myList.append([val['chr'][0], val['position'][0],'.',val['reference'][0], val['alternative'][0],'.','.','.','GT:AD:DP\t%s:%s,%s:%s' % (val['GT'][0], val['AD'][0][0],val['AD'][0][1], val['DP'][0])])
TypeError: 'NoneType' object is not subscriptable

I've used the GATK pipeline in the var_calling.py script for variant calling (except using VCFtools for the last step to retain only PASS SNPs), and my VCF variant lines look like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  hapA
chr88_hapA      42      .       T       C       523.64  PASS    .       GT:AD:DP:FT:GQ:PL       0/1:35,22:57:heterozygous:99:531,0,1333
chr88_hapA      64      .       C       T       689.64  PASS    .       GT:AD:DP:FT:GQ:PL       0/1:42,25:67:heterozygous:99:697,0,1331
chr88_hapA      86      .       T       G       569.64  PASS    .       GT:AD:DP:FT:GQ:PL       0/1:40,22:62:heterozygous:99:577,0,1337

I'm also attaching a small test VCF with only the first 25000 lines for both hapA and hapB, in case those are useful for reproducing the problem (these came from the hapA.pass.snp.vcf and hapB.pass.snp.vcf files). I'm using python 3.6.3.

Thank you!

Edit: after a little more playing around, it appears that this error is connected with using the -amb 1 option. I was able to successfully run the script using -amb 0 and -amb 2.

hapB.small.vcf.gz
hapA.small.vcf.gz

I have a phased triploid genome and re-sequencing reads . Could I use Haplotypo for SNP calling?

Hey thanks for developing this tool! I am very excited to try to use it.
We have assembled a phased genome and we know that the coordinates are not one-to-one and expect large inversions deletions etc...

I read your advice in the FAQ of the wiki and was hoping you could still offer some advice on how to generate the coordinates table file.

I was thinking using NUCmer and show-coords but not sure exactly how to translate to a format that would work with HaploTypo.

I know this is slightly out of scope for the actual function of the software, but was still hoping you could shed some light on this.

Thanks,
Ben