Mosaic pipeline #42
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Mosaic pipeline #42
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Madelinehazel
requested changes
May 4, 2022
cre.gemini.variant_impacts.vcf2db.sh
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| @@ -31,10 +31,14 @@ fi | |||
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| #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 && [ "$type" != "wes.mosaic" ]
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Since mosaic pipeline uses only one caller, I didn't set "callers" variable. Therefore there is no callers in gemini db_info
cre.gemini.variant_impacts.vcf2db.sh
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| then | ||
| callers="v.callers" | ||
| caller_filter="and v.callers not in ('freebayes', 'samtools', 'platypus')" | ||
| elif [ ! -z "$callers" ] && [ "$type" == "wes.mosaic" ] |
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If the above is true, you can remove this conditional block
cre.gemini2txt.vcf2db.sh
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| @@ -33,10 +33,14 @@ gemini query -q "select name from samples order by name" $file > samples.txt | |||
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| #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
cre.sh
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| @@ -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?
Madelinehazel
approved these changes
May 17, 2022
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added mosaic option to generate wes.mosaic report