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-   -   Help with HapTree reads input format (http://seqanswers.com/forums/showthread.php?t=51359)

Phoenix_ICE 03-26-2015 04:00 AM

Help with HapTree reads input format
 
Dear All,

I am going to try HapTree to phase the SNP/MNP/InDel/Complex in my VCF, and want to give HapTree a try. But I really have no idea how to prepare the reads input (instead of BAM or fragment file) for HapTree v0.1 (as v1 only support diploid). Would someone help?

Here is a part of the format from examples:

{9: 1, 4: 0}
{0: 1, 1: 0, 4: 0}
{8: 1, 4: 0}
{2: 1, 3: 1}
{9: 0, 4: 1}
{2: 0, 3: 0, 5: 1, 6: 0, 7: 1}
{2: 1, 3: 1}
{5: 1, 6: 0, 7: 1}
{3: 1, 5: 0, 6: 1, 7: 0}
{2: 1, 3: 1}
{2: 1, 3: 1, 6: 0, 7: 1}
{2: 0, 3: 0, 5: 1, 6: 0, 7: 1}
{1: 0, 2: 1, 3: 1, 5: 0, 6: 1}

........

What does the number mean? That really needs an good manual for that.

Please help, any idea?

Phoenix_ICE 03-26-2015 04:08 AM

The first number might refer to the Num-th line in VCF, and the second number might refer to the alleles, each line might refers to an alignment?

How to indicate a Paired END?

Mel Martin 09-28-2016 06:19 AM

Hi Phoenix,
I see that your post is 1 year old but did you found an answer to your question?
Thanks
Mel


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