hardfilter error
I got the vcf file without Picard addgroup before making it. but I realized that it was wrong while making hard filter. I did some research and they told me to do a recall bam but I searched and couldn't find any information about it. Can you help me with this issue?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
gff3 to gtf
written by bestone •
-
gatk Hardfilter Error
written by bestone •
-
TPMCalculator returns zero for some genes, which are non-zero with Cuffdiff (FPKM).
written by Daisuke •
-
Phylip file
written by Kagisoralph •
-
Picard ValidateSamFile Error: "ValidateSamFile Value was put into PairInfoMap more than once"
written by stephen.johnson.online •
-
How to add sequence information to vcf from MPileup
written by helge.fluess •
-
Issues with Variant Calling from old bam files
written by williamsbrian5064
-
Picard ValidateSamFile error
written by boyu93 •
-
best way to interpret RNA-seq after counts and differential expression results?
written by galkimhi123 •
-
Hadoop Bam with .bam files
written by shalini.ravishankar •
I think you are asking about how to add
ReadGroupsto an existing BAM. If that is true then you need this: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-Thank you for your reply, Actually, I wanted to ask. After making Picard Markduplicates, I got a vcf file directly with gatk without making ReadGroups, so I made a mistake. People said that I could fix this error by doing a recall bam, but I couldn't find any information about it. how can I fix this error?
because when I hardfilter the vcf file I saw that I made a mistake