Martin1

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Martin1
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  • Thanks for your respons Geraldine! I've found a way to do what I wanted by cheating the genelist option. using awk I converted my exon bedfile to refseq format with the following command: awk -F $'\t' 'BEGIN {OFS = FS} {split($4,genename,"_&qu…
  • Hi Geraldine, Problem is solved with -rf BadCigar but haplotypecaller also failed for the same reason, bad cigar strings. I'm now trying with bwa mem 0.7.4 to see if that also resolves the problem. Regards
  • Thank you Geraldine :)
  • Hello, I have the same problem and I also did (full)validation of my bam file using picard tools. That gave me a few of these: ERROR: Record 101395, Read name D5N3XBQ1:209:C1NN9ACXX:8:2107:15007:47976, NM tag (nucleotide differences) in file [1] …
  • Hello, I have the same error for version 2.5.2. I my case it happens with the BaseRecalibrator: INFO 15:58:09,019 HelpFormatter - -------------------------------------------------------------------------------- INFO 15:58:09,023 HelpFormatter - …