behzad
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Latest activity by behzad-
behzad created a post,
error when running ASEReadCounter
Hello, I am trying to run ASEReadCounter (GATK_4_2_1_0) using the following command: gatk ASEReadCounter \\ -R ${params.genome} \\ -V ${params.vcf_infile} \\ ...
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behzad commented,
Hi Anthony Dias-Ciarla , I have tried many times to send you the full log message but apparently cannot be submitted. is there any way that I can attach a text file (containing the log message)? ot...
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behzad commented,
Hi Anthony Dias-Ciarla I put all log message. the following lines with dots that you see in the log output like the following represent to many lines in the log output which are similar to the line...
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behzad created a post,
incomplete output when running ASEReadCounter
AnsweredI am using gatk ASEReadCounter to get the read counts per allele using this command: gatk ASEReadCounter -R /path_to_genome/hg38_genome/GRCh38.p13.genome.fa -I sample.sorted.bam -V sample.vcf.gz...
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behzad commented,
Hi Genevieve Brandt (she/her) , Thanks. that worked! I have another problem now. after running the command in my first question, I got it working but at some point it gave error and the resulting o...
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behzad commented,
Hi Genevieve Brandt (she/her) , sorry, It is now corrected. Thanks Behzad
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behzad commented,
Hi Genevieve Brandt (she/her) , I have updated the main question with the log output. now , would you please let me know what the problem could be? Thanks, Behzad
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behzad commented,
Hi Genevieve Brandt (she/her) , sure the following is the log output. the rest of required information are mentioned in previous message. java -Dsamjdk.use_async_io_read_samtools=false -Dsamjd...
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behzad commented,
Hi Genevieve Brandt (she/her) I do not have any log file after running the command. shall i add any argument to the command to get log file as well? Thanks, Behzad
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behzad created a post,
no read counts per allele while using gatk ASEReadCounter
AnsweredI am using gatk ASEReadCounter to get the read counts per allele. To do so, I used the following command: gatk ASEReadCounter -R /path_to_genome/hg38_genome/GRCh38.p13.genome.fa -I sample.sorted....