Parsimony

[Jordi-V]

Dear all,

I just only want to know, if pre.py realize the parsimony step for normalize... If is yes, i just only want to know which flag is related to parsimony... because in the following example in my opinion dont apply the parsimony... We ran pre.py like this: pre.py sample.vcf.gz sample.vcf_normalization.gz -r genome_women.fa -L --pass-only --threads 2

We did different proves like without -L or applying the --bcftools-norm and we get the same results...

5044138 G A,GATATA NO normalize (original vcf) 5044138 G A After pre.py apply 5044138 G GATATA After pre.py apply 6161100 T TTA,TTTA No normalize (original vcf) 6161100 T TTA,TTTA After apply pre.py 7332729 T TTG,TTTG 7332729 T TTG,TTTG

In the second example I suppose that the output must be like this:

6161100 T TTA 7332729 T TTG And appear: 6161100 T TTA,TTTA 7332729 T TTG,TTTG

and in my opinion this is not correct, not apply the parsimony... and decompose too...

The second question is about if I can run hap.py only for normalize my samples, without compare with a thruth set... Run exactly the same as pre.py?

Thanks a lot for your help

Jordi

[Jordi-V]

Sorry I found another question....

The vcf without apply normalization with pre.py i I've this output:

22 16371684 . CAAAAAAAAAAAAA C,CAAAAAAAAAAAAAAAAAAA GT 1/2

after normalize with pre.py:

22 16371684 . CAAAAAAAAAAAAA C GT 0/1

Why delete de second allele?? Is different from the first, because the first is a deletion and second an insertion right? It is not correct decompose in two lines?? The genotype is different and its correct I suppose...

I'm sorry but I dont understand...

Thanks jordi

[Jordi-V]

Sorry for insistence, but could anyone help me...

Thanks

[Jordi-V]

Dear all,

someone could answer the question?? I will appreciate.... Thanks