Hello again, I successfully run the aberrantSplicing module, now I'm trying to run mae. However it gives errors while mae_createSNVs and mae_allelicCounts.
These are parameters in config.yaml:
mae:
run: true
groups:
- mae
gatkIgnoreHeaderCheck: true
padjCutoff: 0.05
allelicRatioCutoff: 0.7
addAF: false
maxAF: 0.001
maxVarFreqCohort: 1
qcVcf: /home/arda/rnaseq/gencode29/qc_vcf_1000G_GRCh38.vcf.gz
qcGroups:
- mae
dnaRnaMatchCutoff: 0.85
I attached the sample annotation and log files also.
2025-08-08T144907.080231.snakemake.log
sample_annotation_new1.txt
According to previous issues, I get the bam files with read groups but it didnot work. Both vcf and bam files are in same format (chr1, chr2).
In this case, 3618 and 3619 are controls, while 3620 replicas are proband. Also, I have only vcf file of 3620.
What is the source of the error and how can I fix it?
Thanks.
Hello again, I successfully run the aberrantSplicing module, now I'm trying to run mae. However it gives errors while mae_createSNVs and mae_allelicCounts.
These are parameters in config.yaml:
mae:
run: true
groups:
- mae
gatkIgnoreHeaderCheck: true
padjCutoff: 0.05
allelicRatioCutoff: 0.7
addAF: false
maxAF: 0.001
maxVarFreqCohort: 1
qcVcf: /home/arda/rnaseq/gencode29/qc_vcf_1000G_GRCh38.vcf.gz
qcGroups:
- mae
dnaRnaMatchCutoff: 0.85
I attached the sample annotation and log files also.
2025-08-08T144907.080231.snakemake.log
sample_annotation_new1.txt
According to previous issues, I get the bam files with read groups but it didnot work. Both vcf and bam files are in same format (chr1, chr2).
In this case, 3618 and 3619 are controls, while 3620 replicas are proband. Also, I have only vcf file of 3620.
What is the source of the error and how can I fix it?
Thanks.