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Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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QUAL value missing in only-tumor model #190

Closed shiwanyin closed 5 years ago

shiwanyin commented 5 years ago

Hello~

when I use Tumor-Only Analysis , the values in QUAL Colum are null. So i want to know how to display the value in QUAL colum or is it not displayed in Tumor-Only Analysis ? cmd line and output records such as :

cmdline=/opt/Software/miniconda2/pkgs/manta-1.5.0-py27_0/bin/configManta.py --tumorBam HD753_S3.sorted.markdup.bam --referenceFasta /mnt/databaseNGS/reference/ucsc.hg19.fasta --runDir HD753_S3 --exome

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HD753_S3

chrM 7791 MantaBND:5:0:1:0:5:0:1 C ]chr4:55598062]C . PASS SVTYPE=BND;MATEID=MantaBND:5:0:1:0:5:0:0;CIPOS=0,11;HOMLEN=11;HOMSEQ=CCGCCATCATC;BND_DEPTH=51;MATE_BND_DEPTH=4805 PR:SR 548,1:3256,2

Thanks!

x-chen commented 5 years ago

QUAL is currently not calculated under tumor-only mode.

shiwanyin commented 5 years ago

ok, thanks