No variants called, but no error message

[ellalalalalalala]

Hi :) In the past, I always used Jacusa1. After having some problems with not called variants, I decided to test the new Jacusa2 version.

I used the latest version (2.0.2) with the following command: java -Xmx160g -jar $directory/JACUSA_v2.0.2-RC.jar call-2 -m 30 -q 25 -c 10 -a H:condition=1,M,B,Y -F 3 -T 1.56 -f V -r SNPs_name.out $RNA1.bam $RNA2.bam

My input files are both BAM files, which were already deduplicated , sorted and indexed via samtools (after mapping via BBMAP). The same input files (and Jacusa settings) worked perfectly with Jacusa1.

The execution of my script did not result in any error messages but the output vcf files does not contain any variants:

_##fileformat=VCFv4.2

FILTER=<ID=B,Description="Filter potential false positive variants adjacent to read start/end.

| :distance Filter base calls within distance to feature. Default: 6 | :minRatio Minimal ratio of base calls to pass filtering. Default: 0.5 ">

FILTER=<ID=H,Description="Filter non-homozygous sites in condition 1 or 2.

| :condition Possible values for condition: 1 or 2. (Required) ">

FILTER=<ID=M,Description="Max allowed alleles per site.

| :maxAlleles must be > 0. Default: 2 ">

FILTER=<ID=Y,Description="Filter wrong variant calls within homopolymers.

| :length must be > 0. Default: 7 ">

FORMAT=

FORMAT=

FORMAT=

contig=

contig=

[...... other contigs listed......]

contig=

contig=

fileDate=20210616

source=JACUSA2 Version: 2.0.2-RC call-2 -m 30 -q 25 -c 10 -a H:condition=1,M,B,Y -F 3 -T 1.56 -f V -r SNPs_BBmap_BBDUK-IMR2_jacver2-test1_RNARNA_custrans_15072021_2021-07-15.out mapped_BBmap_BBDUK-RNAwt_jacver2-test1_IMR2_custrans_15072021_2021-07-15.sam-fixmate-sorted-deduped.bam mapped_BBmap_BBDUK-IMR2_jacver2-test1_RNAsample_custrans_15072021_2021-07-15.sam-fixmate-sorted-deduped.bam

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 11 21_

Did I make a mistake? Are there any ideas on how I could solve the problem?

Thanks a lot in advance and have a nice day :)

[piechottam]

Please rerun without "-f V" to check if this is VCF output related.

[ellalalalalalala]

I will do that, thank you!

[ellalalalalalala]

Hi piechottam,

I tried _java -Xmx160g -jar $LOCATION/JACUSAv2.0.2-RC.jar call-2 -m 30 -q 25 -c 10 -a H:condition=1,M,B,Y -F 3 -T 1.56 -r SNPs"$name""$date".out $RNA2 $RNA1

This time, the output file looks like that:

_## JACUSA2 Version: 2.0.2-RC call-2 -m 30 -q 25 -c 10 -a H:condition=1,M,B,Y -F 3 -T 1.56 -r SNPs_BBmap_BBDUK-IMR2_jacver2-test1_RNARNA_custrans_22072021_2021-07-22.out /scratch/hpc-prf-ptma2/ptma2001/bbmap/mapped_BBmap_BBDUK-RNAwt_jacver2-test1_IMR2_custrans_15072021_2021-07-15.sam-fixmate-sorted-deduped.bam /scratch/hpc-prf-ptma2/ptma2001/bbmap/mapped_BBmap_BBDUK-IMR2_jacver2-test1_RNAsample_custrans_15072021_2021-07-15.sam-fixmate-sorted-deduped.bam

contig start end name score strand bases11 bases21 info filter ref_

[ellalalalalalala]

The Output was empty, because -F 3 removed paired reads. Without -F 3 it works :)

Thanks a lot for the great support! 💯