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Snakemake corrections #50
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...to allow it to be submitted as a cluster job since we don't specify it as a local rule anymore.
The configuration option in config.yaml needs to match the name of the snakemake rule, which doesn't have a '2' in it.
Thanks for merging. There's one more outstanding issue-- this code passes the same GATK jar file to both SomaticSeq and Mutect2, but SomaticSeq cannot work with GATK4. This problem would go away if you make that happen. Otherwise, it's probably necessary to have a |
I'll see if I can switch out GATK3 to GATK4 (i.e., GATK3's CombineVariants
to GATK4's MergeVcfs).
Best,
…On Thu, Jan 25, 2018 at 3:36 PM, Afif Elghraoui ***@***.***> wrote:
Thanks for merging. There's one more outstanding issue-- this code passes
the same GATK jar file to both SomaticSeq and Mutect2, but SomaticSeq
cannot work with GATK4. This problem would go away if you make that happen.
Otherwise, it's probably necessary to have a gatk3 config setting as well
as a gatk4 setting rather than just one for both. Do you think it's worth
making this split now, or is an update to GATK4 in the SomaticSeq wrapper
coming soon?
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That'd be great. Thanks! |
Hi Afif,
I've been using GATK3's CombineVariants to merge VCF files. GATK4 doesn't
have its equivalent. I could switch out GATK3 CombineVariants, but that'll
probably take me a little while to do and then validate.
So for now, should I still merge your pull request?
Best,
…On Fri, Jan 26, 2018 at 11:33 AM, Afif Elghraoui ***@***.***> wrote:
That'd be great. Thanks!
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#51? Well, I guess for now, it would break if anyone tried to run it as written, so maybe it's not a good idea to document it while it's known to be broken. On the other hand, I saw that you did have support for running SomaticSeq without GATK at all, so maybe we should just not pass |
Yes, we can do that, not having --gatk argument at all.
Without --gatk, it'll just cat all the VCF and then sort using this command:
cat $all_snp | egrep -v '^#' | awk -F "\t" '{print $1 "\t" $2 "\t.\t" $4
… "\t" $5}' | sort | uniq | awk -F "\t" '{print $1 "\t" $2 "\t" $3 "\t" $4
"\t" $5 "\t" "." "\t" "PASS" "\t" "."}' | cat <(echo -e
'##fileformat=VCFv4.1\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO') - |
$MYDIR/utilities/vcfsorter.pl ${hg_dict} - >
${merged_dir}/CombineVariants_MVJSD.snp.vcf
On Thu, Feb 15, 2018 at 1:08 PM, Afif Elghraoui ***@***.***> wrote:
#51 <#51>? Well, I guess for
now, it would break if anyone tried to run it as written, so maybe it's not
a good idea to document it while it's known to be broken.
On the other hand, I saw that you did have support for running SomaticSeq
without GATK at all, so maybe we should just not pass --gatk to the
invocation of the SomaticSeq wrapper until GATK4 support there is ready.
What do you think about that?
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Ok. I'll file an issue for this GATK4 thing just for tracking purposes, and then I'll add another commit to #51. |
minor bugs in the workflow that would cause it to error out in some cases.