Test file variants found not the same as manual

[Julia]

Hi,

When I found out about Cake, I was very excited to give it a try on my brain tumour exome sequences. It sounds like an incredibly valuable pipeline for cancer data.

I think I have Cake installed properly, but when I run the test files, I end up with 0 variants. The variant callers appear to be working as the output files are populated with variants. The intermediate files also have some variants although they are eventually filtered down to 0 variants.

I would be very grateful for any advice on how to troubleshoot as the pipeline seems to run smoothly and I have been unable to locate my problem for many days.

Thank you,
Julia
Garvan Institute

===================================================

My POST_PROCESS_README.txt:

Architecture Information

SYSTEM TYPE => STANDALONE
### ------------------------- ###
### Intersection of Various Callers ###
Callers Files Found => mpileup,bambino,varscan,somaticsniper
VCF TO INTERSECT => 2
### ------------------------- ###
### Species and Reference Genome ###
SPECIES => MOUSE
FASTA => /home/julyin/DIR_TO_TEST_CAKE/software_path/Cake/trunk/test_relevant_files/Reference_Fasta_Files/GRCm38_um_just_sliced_chr19.fa
### ------------------------- ###
### Filter Status ###
EXONIC FILTER FLAG => TRUE
SNP FILTER FLAG => TRUE
INDEL FILTER FLAG => TRUE
GERMLINE FILTER FLAG => TRUE
BASE-POS FILTER FLAG => TRUE
SOMATIC COVERAGE FILTER FLAG => TRUE
CONSEQUENCE ANNOTATE FLAG => FALSE
CONSEQUENCE FILTER FLAG => FALSE
VARIANT ALLELE RATIO FILTER FLAG => TRUE
### ------------------------- ###
### Variant Calling Parameters ###
MINIMAM MAPPING QUALITY => 15
MIN_NUCLEOTIDE_QUALITY => 10
MIN_COVERAGE => 4
### ------------------------- ###
### Bambnino Specific Paramters ###
MIN FLANKING QUALITY => 15
MIN_ALT_ALLELE_COUNT => 2
MIN_MINOR_FREQUENCY => 0
MMF_MAX_HQ_MISMATCHES => 5
MMF_MIN_HQ_THRESHOLD => 15
MMF_MAX_LQ_MISMATCHES => 6
UNIQUE_FILTER_COVERAGE => 2
### ------------------------- ###
### Mpileup Specific Paramters ###
BWA_DOWNGRADE_COFF => 50
NO_OF_READS_TO_CONSIDER_REALIGNMENT => 3
FREQ_OF_READS => 0.0002
MPILEUP_QUALITY_THRESHOLD => 10
### ------------------------- ###
### Caveman Specific Paramters ###
NO_OF_BASES_TO_INCREMENT => 250000
### ------------------------- ###

### Various Filtering Information and Files ###

GENOMES =>
KNOWN_MOUSE_SNP => /home/julyin/DIR_TO_TEST_CAKE/software_path/Cake/trunk/test_relevant_files/SNP_Files/Test_SNP_File.pos

EXON FILE => /home/julyin/DIR_TO_TEST_CAKE/software_path/Cake/trunk/test_relevant_files/Exon_Interval_Files/Test_exonic_cordinate_file.interval
INDEL FILE => /home/julyin/DIR_TO_TEST_CAKE/software_path/Cake/trunk/test_relevant_files/InDel_File/Test_Indel_interval_file.interval
MIN_BASE_POSITION_FREQUENCY => 0.6
Variant Filtering [ Post Processing ] Parameters
Variant Allele Ratio Filter Type => VAR
Variant Allele Ratio Filter Threshold => 0.1

[geNomeBD]

Hi Julia,
Probably answered this you by email few months ago.

The Smaller BAM files were chosen for easier data sharing purpose and just to give a quick start purpose. Switching off couple of filtering modules gives you that result.
I am trying to upload some bigger BAMs to the test files directory.

Thanks,
Mamun