Question: pindel output error
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gravatar for Bioblazer
14 months ago by
Bioblazer50
Pune
Bioblazer50 wrote:

i have been running pindel like so:

./pindel -f h3rv.fasta -i bam_config.txt -c ALL --Ploidy ploidy_input.txt -o Result_pindel.out

-- this is part of bam_config.txt

/biobank/seq/muthuk/Mycobacterium_bovis/R100/bamfiles/sorted_bam/SRR5216939_mapped.sort.bam 241.4 
SRR5216939
/biobank/seq/muthuk/Mycobacterium_bovis/R100/bamfiles/sorted_bam/SRR5216940_mapped.sort.bam 242.9 
SRR5216940

2 Ids path of bam file along with insert size and sample ID.

Here I used 192 samples but the output shown result only for 10 entries in VCF file

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  .0      .1      .2      .3      .4      .5      .6      .7      .8      .9
NC_000962.3     84      .       CG      C       .       PASS    END=85;HOMLEN=1;HOMSEQ=G;SVLEN=-1;SVTYPE=DEL    GT:AD   0/0:1252,0      0/0:1025,0      0/0:1306,0      0/0:1345,0      0/0:1427,0      0/0:1464,1      0/0:1466,0      0/0:678,0       0/0:2056,0      0/0:1150,0

Please anybody tell me what went it wrong here and suggest the steps to be followed. Thanks in advance.

next-gen alignment genome • 539 views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 14 months ago by Bioblazer50

run samtools view -H and check the read groups RG in the bam header. Is there 192 distinct SN names ?

ADD REPLYlink modified 12 months ago • written 12 months ago by Pierre Lindenbaum117k
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