1. Community
2. General Discussion
3. BaseRecalibrator error

Hi Tanay, How did you solve this problem? I am facing same problem.

• View comment
• Niharika
• December 04, 2023 19:42
• 0 votes

1. Community
2. Germline
3. CombineGVCFs - KEY END found in VariantContext field INFO but this key isn't defined in the VCFHeader

Hi Ryan Sun will you please tell me how did you add END tag in the VCF? Also I would like to know if you got an end key reported in vcf at the position where error is thrown? I can not see any END ...

• View comment
• Niharika
• December 02, 2023 19:23
• 0 votes

1. Tool Index
2. 4.0.9.0
3. SplitNCigarReads

I am using GATK SplitNCigarReads version 4.0.5.1 And getting an error (attached) gatk SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_unique_reads_with...

• View comment
• Niharika
• December 01, 2023 12:46
• 0 votes

1. Community
2. Other
3. GATK BQSR is taking too long to be run (running since last 6 days)

Hello, Using sorted bam solved my problem

• View comment
• Niharika
• December 01, 2023 12:08
• 0 votes

1. Community
2. Other
3. Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException

Hi I am using GATK SplitNCigarReads version 4.0.5.1 And getting an error (attached) gatk SplitNCigarReads -R SplitNCigar_Reads/human_genome.fna -I Mark_duplicates/PicardOutput/sorted_unique_reads_w...

• View comment
• Niharika
• November 30, 2023 13:23
• 0 votes

1. Tool Index
2. 4.1.4.1
3. Mutect2

Can this tool be used to call variants from multiple samples? By multiple samples I mean multiple individuals.

• View comment
• Niharika
• November 10, 2023 05:17
• Edited
• 0 votes