WorkArounds for Bugs in Version 1.07

[Mary Kate Wing]

I have gotten a couple of emails from people who have encountered minor issues with the latest version.

I have added updated the GotCloud FAQ wiki page with these issues & appropriate work arounds.

I just wanted to share those with you:  http://genome.sph.umich.edu/wiki/GotCloud:_FAQs#Version_1.07

Let me know if you encounter any additional issues.

The 2 issues that have been encountered so far:

1. Type of arg 1 to keys must be hash (not hash element) at gotcloud/bin/Conf.pm line 155, near "}) "
Compilation failed in require at gotcloud/bin/align.pl line 56.

To fix this bug, you need to edit gotcloud/bin/Conf.pm, line 155.  This error only occurs with certain versions of perl.

Change

foreach my $key (keys $CONF_HASH{$section}) {

to

foreach my $key (keys %{$CONF_HASH{$section}}) {

2. Illegal division by zero at gotcloud/scripts/vcf-summary line 388.
make: *** [vcfs/chrY/chrY.hardfiltered.vcf.gz.OK] Error 255
make: *** Waiting for unfinished jobs....
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:

CHRS = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

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:

PED_INDEX = pedigreeFile.ped

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.