Hi,
Sorry about this. In practice, I could not think about all cases. I'll try
to make the change in the new release.
Olivier.
On 14 November 2013 19:12, endrebak <[log in to unmask]> wrote:
> Hi--
>
> the problem seemed to be that shapeit convert did not accept lists of one
> individual that ended with a newline. Perhaps this part can be made more
> robust by accepting both versions?
>
> Anyways, now it all works fine. Thanks for an excellent program.
>
> Endre
>
>
> On 2013-11-13 23:07, endrebak wrote:
>
>> Hello--
>>
>> I want to implement a "leave one out" imputation pipeline- that is, I
>> want to impute all the individuals in the study, using all the other
>> individuals as reference. This is where the -convert option comes in
>> handy; when I want to impute into individual X, I just pick out the
>> phased haplotype from individual X with the convert option.
>>
>> However, for some reason, it is not producing the correct output.
>>
>> I use the command "shapeit.v2.r727.linux.x64 --input-bed
>> {params.prefix}.bed {params.prefix}.bim {params.prefix}.fam -M
>> {input.map_of_recombination_rates} --output-max {output} --thread
>> {threads}" on some unphased binary plink files to produce a haps and
>> sample file as shown here (truncated with head and cut):
>> http://pastebin.com/y6G6B9YN So far, so good.
>>
>> Next, I want to extract a single individual, let's say 11464_ATCACG
>> from the haps, sample files. For this, I use the command:
>> "shapeit.v2.r727.linux.x64 -convert --input-haps {{params.input_haps}}
>> --output-haps {{params.output_haps}} --include-ind {sample_id}"
>>
>> (The {sample_id} file is just a file containing the text 11464_ATCACG\n.)
>>
>> The log file for this operation is shown here:
>> http://pastebin.com/S9EzgeSH
>>
>> Problem is, the sample file produced looks like
>>
>> ID_1 ID_2 missing father mother sex plink_pheno
>> 0 0 0 D D D B
>>
>> and the (head of the) haps file produced looks like
>>
>> 20 20:63244 63244 C A
>> 20 20:68396 68396 T C
>> 20 20:76771 76771 T C
>> 20 20:91088 91088 C T
>> 20 20:100505 100505 C T
>> 20 20:100699 100699 T C
>> 20 20:102181 102181 C T
>> 20 20:126149 126149 C T
>> 20 20:126224 126224 G A
>> 20 20:127720 127720 A C
>>
>> That is, the sample file is missing its third line, it should look like:
>>
>> ID_1 ID_2 missing father mother sex plink_pheno
>> 0 0 0 D D D B
>> 11464_ATCACG 11464_ATCACG 0 0 0 0 -9
>>
>> and the haps file produced is missing its two last columns, which
>> should contain zeroes and ones.
>>
>> Am I doing something wrong or misunderstanding anything?
>>
>> Thanks,
>>
>> Endre
>>
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--
Olivier DELANEAU
Maître assistant
Département de Génétique et Développement (GEDEV)
1, Michel-Servet, CH-1211 Genève 4
+41 (0) 22 379 55 51
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