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YuSugihara / QTL-seq

QTL-seq pipeline to identify causative mutations responsible for a phenotype
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Bcftools mpileup error #47

Open Tarun-PAU opened 6 months ago

Tarun-PAU commented 6 months ago

please suggest, how to rectify this error.

[QTL-seq:2024-02-09 21:00:33] !!ERROR!! bcftools mpileup -a AD,ADF,ADR -B -q 40 -Q 18 -C 50 -O u -r LR618874.1 -f tarunm/10_ref/maize.fa --ignore-RG tarunm/20_bam/parent.bam tarunm/20_bam/bulk1.bam tarunm/20_bam/bulk2.bam | bcftools call -vm -f GQ,GP -O u | bcftools filter -i "INFO/MQ>=40" -O z -o tarunm/30_vcf/qtlseq.LR618874.1.vcf.gz >> tarunm/log/bcftools.LR618874.1.log 2>&1