Comments (2)
aquaskyline
commented on May 28, 2024
Unable to tell what was wrong without the culprit VCF file. Could you please copy and paste here the VCF records at 103549237 and 10000678, as well as 10 flanking records of the two sites?
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alex538
commented on May 28, 2024
Here are the vcf records.
chr10 103540571 . C T 257 . . GT:GQ:DP 0/1:257:47
chr10 103540586 . A G 210 . . GT:GQ:DP 0/1:210:45
chr10 103540684 . GA G 213 . . GT:GQ:DP 0/1:213:39
chr10 103540789 . C T 246 . . GT:GQ:DP 0/1:246:42
chr10 103543641 . G A 261 . . GT:GQ:DP 0/1:261:34
chr10 103545244 . G T 200 . . GT:GQ:DP 0/1:200:39
chr10 103547827 . T G 448 . . GT:GQ:DP 1/1:448:41
chr10 103547967 . G A 273 . . GT:GQ:DP 0/1:273:39
chr10 103548132 . T C 999 . . GT:GQ:DP 1/1:999:49
chr10 103548331 . C CT 105 . . GT:GQ:DP 1/1:105:70
chr10 103549106 . C G 999 . . GT:GQ:DP 1/1:999:51
chr10 103549237 . T A 271 . . GT:GQ:DP 0/1:271:35
chr10 10000678 . C T 232 . . GT:GQ:DP 0/1:232:40
chr10 10000703 . C CGTGT 91 . . GT:GQ:DP 0/1:91:60
chr10 10000862 . T C 265 . . GT:GQ:DP 0/1:265:30
chr10 10000931 . A G 265 . . GT:GQ:DP 0/1:265:45
chr10 10001196 . T A 213 . . GT:GQ:DP 0/1:213:43
chr10 10001623 . A T 251 . . GT:GQ:DP 0/1:251:35
chr10 10001745 . G T 143 . . GT:GQ:DP 1/1:143:35
chr10 10001859 . C T 235 . . GT:GQ:DP 0/1:235:29
chr10 10002770 . ATG A 134 . . GT:GQ:DP 0/1:134:37
chr10 10002942 . T C 237 . . GT:GQ:DP 0/1:237:47
chr10 10003182 . A G 280 . . GT:GQ:DP 0/1:280:53
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Related Issues (20)
- program crashes internally but still writes VCF and successfully returns 0 HOT 1
- High runtime, high memory, low precision and recall using NA12878 data HOT 2
- GetTruth.py: error: unrecognized arguments: --noGT 1 HOT 13
- cannot connect to X server localhost HOT 2
- trainedModels directory HOT 1
- TrainingModels and new Bam file HOT 1
- Non-human data? HOT 1
- callVarBam.py fails with taskset: failed to set pid 0's affinity: Invalid argument HOT 1
- SNV report is not consistent with the bam file HOT 1
- Is model of human genome applicable to variant calling on bacterial data ? HOT 1
- Applying full support for the IUPAC nucleotide code standard for better robustness? HOT 4
- Does the pacBio model you have trained can be used for PacBio CCS reads? HOT 1
- GPU conda install docs remove Clairvoyante HOT 2
- How is the QUAL metric calculated? HOT 2
- Check that BAM is indexed HOT 1
- PyPy HOT 1
- PacBio hifi HOT 1
- BAM:the genome region you specified has no read cover HOT 2
- No output in commands.sh HOT 1
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