Activity for Xavier Argout
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Xavier Argout posted a comment on discussion Frequently Asked Questions
Dear Jorge, thank you for your advice. I sorted again the Bowtie2 sam files with Picard tools and MultisampleVariantsDetector now works!!! Problem solved! Thank you, Xavier
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Dear Jorge, it is the same reference file I used for mapping and for NGSEP. Please find attached chr1.fa
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Dear Jorge, it is the same reference file I used for mapping and for NGSEP. Please find attach chr1.fa
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Dear Jorge, thank you for your prompt answer. Yes it was a typo in my message, sorry. Mapping was done with Bowtie2 (in paired mode) and Bam files were generated with samtools : command line : samtools view -u CCKM23-041.header.sam | samtools sort -o CCKM23-041.sorted.bam Attached is the result of your command . Thanks again for your help. Xavier
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Dear NGSEP team, I have just experienced a problem with the MultisampleVariantsDetector module. The analysis of 95 sorted bam samples with header seemed to run fine and finished with the message "INFO: Multisample Variants Detector Completed". The generated VCF file contained only the header lines, but no data lines with information about the SNP markers. The command line I used was java -jar NGSEPcore4.3.2.jar MultisampleVariantsDetector -r Theobromacacaocriollochr.v2.0.fna -maxAlnsPerStartPos 1000...
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Dear NGSEP team, I just experience a problem with the MultisampleVariantsDetector module. Analysis done on 95 sorted bam samples with header seemed to run without problem and finished with a "INFO: Multisample Variants Detector Completed" message. The generated VCF file just contained the head lines but no data lines containing information about the SNP markers. The command line I used was this one : java -jar NGSEPcore4.3.2.jar MultisampleVariantsDetector -r Theobromacacaocriollochr.v2.0.fna -maxAlnsPerStartPos...
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