bcftools norm -m -any And check for duplicate CHROM, POS, REF, ALT I will try this and report back Author eturro commented Dec 2, 2014 Even with the above attempted workaround, I still get duplicate records. Here is a quasi-minimal example: $ bcftools view -H file1.vcf.gz 1 13946...
bcftools norm New--multi-overlapsoption allows to set overlapping alleles either to the ref allele (the current default) or to a missing allele (#1764and#1802) Fixed a bug in-m -which does not split missingFORMATvalues correctly and could lead to emptyFORMATfields such as::instead of the ...
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vcfnorm.o: vcfnorm.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_faidx_h) $(htslib_khash_str2int_h) $(bcftools_h) rbuf.h vcfquery.o: vcfquery.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_khash_str2int_h) $(htslib_vcfutils_h) $(bcftools_h) $(...
som_norm_counts(args->som[i]); if ( args->prefix ) { char *bname = msprintf("%s.som.%d", args->prefix,i); som_create_plot(args->som[i], bname); free(bname); } }// evaluate float *good = (float*) malloc(sizeof(float)*ngood); assert(good); ...
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ #include <stdio.h> #...
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/vcfquery.c at 6b
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vcfnorm.c.pysam.c vcfplugin.c vcfplugin.c.pysam.c vcfquery.c vcfquery.c.pysam.c vcfroh.c vcfroh.c.pysam.c vcfsom.c vcfsom.c.pysam.c vcfsort.c vcfsort.c.pysam.c vcfstats.c vcfstats.c.pysam.c vcfview.c vcfview.c.pysam.c vcmp.c vcmp.c.pysam.c vcmp.h version.c ve...
vcfnorm.c.pysam.c vcfplugin.c vcfplugin.c.pysam.c vcfquery.c vcfquery.c.pysam.c vcfroh.c vcfroh.c.pysam.c vcfsom.c vcfsom.c.pysam.c vcfsort.c vcfsort.c.pysam.c vcfstats.c vcfstats.c.pysam.c vcfview.c vcfview.c.pysam.c vcmp.c vcmp.c.pysam.c vcmp.h version.c ver...