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: Work arounds:
: Work arounds:
:: * Disable Chromosome Y by adding the following to your configuration file:
::* Disable Chromosome Y by adding the following to your configuration file:
::: <pre>CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X</pre>
::: <pre>CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X</pre>
::: You may also want to remove the X from the end, since it may be slightly misleading since it assumes all people are female.
::: You may also want to disable chr X since it may be slightly misleading due to the assumption that all samples are female.
:: * Specify a pedigree file that tells GotCloud which individuals are Male & which are Female by adding the following to your configuration file:
::* Specify a pedigree file that tells GotCloud which individuals are Male & which are Female by adding the following to your configuration file:
::: <pre>PED_INDEX = pedigreeFile.ped</pre>
::: <pre>PED_INDEX = pedigreeFile.ped</pre>
::: GotCloud only looks at the 2nd & 5th columns of the pedigree file (white-space delimited)
:::* 2nd column is the individual ID which should match the 1st column of the BAM_INDEX file.
:::* 5th column is the sex, use: 1 for male and 2 for female.
