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Mosaic pipeline #42

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Mosaic pipeline #42

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04481d2
modify scripts to generate mosaic variant report
pamelaxu213 Mar 16, 2022
f0d699b
added mosaic caller
pamelaxu213 May 4, 2022
79393d1
removed redundant line
pamelaxu213 May 17, 2022
08c5cc1
add comments
pamelaxu213 May 17, 2022
71931d9
allows report generation when spliceAI is NA
pamelaxu213 Aug 3, 2022
4427b5e
add mosaic-panel functionality
pamelaxu213 Aug 15, 2022
08fd917
Fixed bug by making columns character in read.delim()
pamelaxu213 Aug 30, 2022
ccbdab7
remove unnessecary lines
pamelaxu213 Aug 31, 2022
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6 changes: 5 additions & 1 deletion cre.gemini.variant_impacts.vcf2db.sh
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Expand Up @@ -31,10 +31,14 @@ fi

#if pipeline is cre, filter out variants only called by one of freebayes, samtools, platypus
callers=`gemini db_info $file | grep -w "variants" | grep -w "callers"`
if [ ! -z "$callers" ]
if [ ! -z "$callers" ] && [ "$type" != "wes.mosaic" ]
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Does 'callers' exist in the mosaic gemini db? If so you can remove && [ "$type" != "wes.mosaic" ]

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@pamelaxu213 pamelaxu213 May 17, 2022 •
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Since mosaic pipeline uses only one caller, I didn't set "callers" variable. Therefore there is no callers in gemini db_info

then
callers="v.callers"
caller_filter="and v.callers not in ('freebayes', 'samtools', 'platypus')"
elif [ ! -z "$callers" ] && [ "$type" == "wes.mosaic" ]
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If the above is true, you can remove this conditional block

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done

then
callers="callers"
caller_filter=""
else
callers="00"
caller_filter=""
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6 changes: 5 additions & 1 deletion cre.gemini2txt.vcf2db.sh
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Expand Up @@ -33,10 +33,14 @@ gemini query -q "select name from samples order by name" $file > samples.txt

#if pipeline is cre, filter out variants only called by one of freebayes, samtools, platypus
callers=`gemini db_info $file | grep -w "variants" | grep -w "callers"`
if [ ! -z "$callers" ]
if [ ! -z "$callers" ] && [ "$type" != "wes.mosaic" ]
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same comments as above

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done

then
callers="callers"
caller_filter="and Callers not in ('freebayes', 'samtools', 'platypus')"
elif [ ! -z "$callers" ] && [ "$type" == "wes.mosaic" ]
then
callers="00"
caller_filter=""
else
callers="00"
caller_filter=""
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5 changes: 4 additions & 1 deletion cre.sh
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Expand Up @@ -7,7 +7,7 @@
# family = [family_id] (=project_id=case_id=folder_name, main result file should be family/family-ensemble.db)
# cleanup= [0|1] default = 0
# make_report=[0|1] default = 1, don't make report for WGS analysis first
# type = [ wes.regular (default) | wes.synonymous | wes.fast | rnaseq | wgs | annotate (only for cleaning) |
# type = [ wes.regular (default) | wes.synonymous | wes.mosaic | wes.fast | rnaseq | wgs | annotate (only for cleaning) |
# denovo (all rare variants in wgs, proband should have phenotype=2, parents=phenotype1 also sex for parents in gemini.db) ]
# max_af = af filter, default = 0.01
# database = path to folder where c4r count files and hgmd.csv are found.
Expand Down Expand Up @@ -97,6 +97,9 @@ function f_cleanup
ln -s ${family}-precalled.db ${family}-ensemble.db
ln -s ${family}-precalled-annotated-decomposed.vcf.gz ${family}-ensemble-annotated-decomposed.vcf.gz
ln -s ${family}-precalled-annotated-decomposed.vcf.gz.tbi ${family}-ensemble-annotated-decomposed.vcf.gz.tbi
#elif [ "$type" == "wes.mosaic"]
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Can we remove these lines?

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done

#then
#break # skip the rest of loop
else
# we don't need gemini databases for individual variant callers
rm ${family}-freebayes.db
Expand Down