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Old 03-26-2015, 04:00 AM   #1
Phoenix_ICE
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Location: UK

Join Date: Jan 2011
Posts: 14
Default 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?
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Old 03-26-2015, 04:08 AM   #2
Phoenix_ICE
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Default

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?
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Old 09-28-2016, 06:19 AM   #3
Mel Martin
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Location: Netherlands

Join Date: Jul 2016
Posts: 1
Default

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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