table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|bwa_tbz|Collection with the bwa source distribution.|@8b6e2c4916133e1d859c9e812861ce13+70@|
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing aligned bam files.||
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing aligned bam files.||
|reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
</div>
|reference|Collection with reference data (*.fasta.gz, *.fasta.fai.gz, *.dict.gz).|@c361dbf46ee3397b0958802b346e9b5a+925@|
</div>
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing aligned bam files.||
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing aligned bam files.||
-|picard_zip|Collection with the picard binary distribution.||
-|gatk_tbz|Collection with the GATK2 binary distribution.||
+|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
+|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
|known_sites|List of files in the data bundle to use as GATK @-known@ arguments. Optional. |@["dbsnp_137.b37.vcf","Mills_and_1000G_gold_standard.indels.b37.vcf"]@ (this is the default value)|
|regions|Collection with .bed files indicating sequencing target regions. Optional.||
|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
|known_sites|List of files in the data bundle to use as GATK @-known@ arguments. Optional. |@["dbsnp_137.b37.vcf","Mills_and_1000G_gold_standard.indels.b37.vcf"]@ (this is the default value)|
|regions|Collection with .bed files indicating sequencing target regions. Optional.||
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing bam files.||
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing bam files.||
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing bam files.||
table(table table-bordered table-condensed).
|_Parameter_|_Description_|_Example_|
|input|Collection containing bam files.||
-|picard_zip|Collection with the picard binary distribution.||
-|gatk_tbz|Collection with the GATK2 binary distribution.||
+|picard_zip|Collection with the picard binary distribution.|@687f74675c6a0e925dec619cc2bec25f+77@|
+|gatk_tbz|Collection with the GATK2 binary distribution.|@7e0a277d6d2353678a11f56bab3b13f2+87@|
|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
|regions|Collection with .bed files indicating sequencing target regions. Optional.||
|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|
|gatk_bundle|Collection with the GATK data bundle.|@d237a90bae3870b3b033aea1e99de4a9+10820@|
|regions|Collection with .bed files indicating sequencing target regions. Optional.||
|region_padding|Corresponds to GATK @--interval_padding@ argument. Required if a regions parameter is given.|10|