Question: is the output.table correct after BQSR?
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6 months ago by
54354165620
54354165620 wrote:

Hiļ¼Œ

after I ran the BQSR command

gatk --java-options "-Xmx4G" BaseRecalibrator -R /home/riceUsers/fyx/bm4/reference/1_genomic.fna -I 1_dedup.bam --known-sites 1_round1_passed_snp.vcf --known-sites 1_round1_passed_indel.vcf -O 1_round1.table

my cotents of the output.table is as follows,I want to know why there is no other eventtype except the M.

who can give me some advices? thank you.

#:GATKTable:6:1:%s:%s:%.4f:%.4f:%d:%.2f:;
#:GATKTable:RecalTable0:
ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors
A00129.2 M 28.0000 27.2591 5723895938 10039694.00

#:GATKTable:6:3:%s:%d:%s:%.4f:%d:%.2f:;
#:GATKTable:RecalTable1:
ReadGroup QualityScore EventType EmpiricalQuality Observations Errors
A00129.2 11 M 11.0000 112782716 8567228.00
A00129.2 25 M 27.0000 229874406 441995.00
A00129.2 37 M 37.0000 5381238816 1030471.00
bqsr gatk • 140 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum131k • written 6 months ago by 54354165620
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