Question: is the output.table correct after BQSR?
gravatar for 543541656
9 months ago by
54354165620 wrote:


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.

ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors
A00129.2 M 28.0000 27.2591 5723895938 10039694.00

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 • 161 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum132k • written 9 months ago by 54354165620
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