Hi,
Is there a way for filtering/removing the structural variants identified in ChrUn and other random contigs or in non-main chromosomes? I am using hg38 assembly.
Will 'vcftools' --chr filtering work here?
I followed 'https://www.biostars.org/p/201603/#273150'. Tried the below code, but it didn't filter the non-main chromosomes in my vcf.
grep -w '^#\|chr[1-9]\|chr[1-2][0-9]\|chr[X]\|chr[Y]' my.vcf > my_filtered.vcf
Example of Manta vcf:
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Normal1 Tumor1
chr1 30405827 MantaBND:0:70561:70576:1:0:0:0 T ]chr1_KI270760v1_alt:58532]T . PASS SVTYPE=BND;MATEID=MantaBND:0:70561:70576:1:0:0:1;IMPRECISE;CIPOS=-568,568;SOMATIC;SOMATICSCORE=41;BND_DEPTH=54;MATE_BND_DEPTH =24 PR 16,0 26,7
In the case of structural variants, translocation events will be present. So, I will have to remove the random chromosomes from ALT columns too. I am trying to do this to keep only chr1-22, X, Y in the Manta structural vcf file to do a circos plot.
Thanks for the help!
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parvathi.sudha •
try with awk:
$ awk '/^#/ || !/chr[0-9A-Za-z]+_/' test.vcf
This would print header rows of vcf and removes any line with chr(single of multiple number,upper or lower case text), followed by underscore _. Little risky without example data. But removes rows with text such as chrun_ or chr1_KI270760v1_alt:58532
Thanks for the reply. This way the ALT column was not modified. Sorry, I forgot to mention about that. I have modified my question.
Great! This one worked. Thank you!
Personally I prefer to use bcftools rather than regex as it has multithreading capability, can work with bcf files and the syntax is much easier to understand when you are revisiting the script.
Depending on the naming convention of your chromosomes, this will do it
bcftools view -r chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrx,chry in.vcf
Or just remove the "chr" before each number and change the X/Y chromosome names accordingly.
Thanks for the answer. But this removes only the chromosomes in #CHROM position. In the case of structural variants, translocation events will be there (ALT column), so that is not being removed by this method.
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Normal1 Tumor1
chr1 30405827 MantaBND:0:70561:70576:1:0:0:0 T ]chr1_KI270760v1_alt:58532]T . PASS SVTYPE=BND;MATEID=MantaBND:0:70561:70576:1:0:0:1;IMPRECISE;CIPOS=-568,568;SOMATIC;SOMATICSCORE=41;BND_DEPTH=54;MATE_BND_DEPTH=24 PR 16,0 26,7
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