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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