3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Version 1.07
: To fix this bug, you need to edit gotcloud/bin/Conf.pm, line 155.
: To fix this bug, you need to edit gotcloud/bin/Conf.pm, line 155.
:Change
:Change
<syntaxhighlight lang="perl">foreach my $key (keys $CONF_HASH{$section}) {</syntaxhighlight>
:<syntaxhighlight lang="perl">foreach my $key (keys $CONF_HASH{$section}) {</syntaxhighlight>
:to
:to
<syntaxhighlight lang="perl">foreach my $key (keys %{$CONF_HASH{$section}}) {</syntaxhighlight>
:<syntaxhighlight lang="perl">foreach my $key (keys %{$CONF_HASH{$section}}) {</syntaxhighlight>
;Illegal division by zero at gotcloud/scripts/vcf-summary line 388.<br />make<nowiki>:</nowiki> *** [vcfs/chrY/chrY.hardfiltered.vcf.gz.OK] Error 255<br />make<nowiki>:</nowiki> *** Waiting for unfinished jobs....<br />Commands finished in xxxxx secs WITH ERRORS. Check the logs
: The current version does not gracefully handle a chromosome with no variants.
: By default, GotCloud assumes all samples are female, producing no chr Y variants, which will produce this error.
: Work arounds:
:: * 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>
::: You may also want to remove the X from the end, since it may be slightly misleading since it assumes all people are female.
:: * 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>
