Hi, here the pipe...
1) ApplyBQSR
while read -r f1 f2; do ....
${ph6} --java-options ${java_opt1} ApplyBQSR -R ${gnm} -I ${fBAM} -O ${fol5}/${c_applybqsr} -L ${f1} -bqsr ${fol5}/${bqsrrd} --static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 --add-output-sam-program-record --create-output-bam-md5 --use-original-qualities
... done
2) GatherBamFiles
java -Dsamjdk.compression_level=${cl} ${java_opt1} -jar ${ph3} GatherBamFiles ${BQSRs} O=${fol4}/${tofixapplybqsr} CREATE_INDEX=true CREATE_MD5_FILE=true
BQSR variable is all Input chr .bam files
3) ValidateSamFile
java -jar ${ph3} ValidateSamFile I=${tofixapplybqsr} MODE=SUMMARY
4)FixMateInformation
java -jar ${ph3} FixMateInformation I=${tofixapplybqsr} O=${applybqsr} CREATE_INDEX=true CREATE_MD5_FILE=true
5)ValidateSamFile
java -jar ${ph3} ValidateSamFile I=${applybqsr} MODE=SUMMARY
After steps 2 the validation of bam file (step 3) give me an error:
HISTOGRAM java.lang.String
Error Type Count
ERROR:MATE_NOT_FOUND 11647
Then I'm going to fix this error with FixMateInformation (step 4) and trying again to validate my bam, the error is always there!
HISTOGRAM java.lang.String
Error Type Count
ERROR:MATE_NOT_FOUND 11647
This kind of error is important? I'have really to fix it or can I go to the next steps (bam -> gVFC).
Any suggestion how to fix it?
My intervals are: chr1... chr22, chrX, chrY, chrM.
Many thanks
Error details
ERROR: Read name A00125:27:H3JT2DMXX:2:2168:22227:12054, Mate not found for paired read
ERROR: Read name A00125:27:H3JT2DMXX:1:2229:28085:35008, Mate not found for paired read
ERROR: Read name A00125:27:H3JT2DMXX:2:2111:1045:33646, Mate not found for paired read
....