Segmentation fault: 11

[Swati Goyal]

Running verifyBamID on using single sample bam and vcf file with ~50 SNV. Added AF in the info field. 

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 4088028_BC160

 1 76211473 . G A 5613.77 PASS AC=1;ACov=443;AF=0.5;AN=2;BaseQRankSum=14.352;ClippingRankSum=0;DP=434;ExcessHet=3.0103;FS=5.061;GQ=99;MLEAC=1;MLEAF=0.5;MQ=70;MQRankSum=0;QD=13.06;ReadPosRankSum=-0.818;SOR=1.123;TCov=443 GT:AD:DP:GQ:PL:AF 0/1:219,211:430:99:5642,0,5090:0

 4 980971 . T G 16987.8 PASS AC=2;ACov=497.46;AF=1;AN=2;DP=513;ExcessHet=3.0103;FS=0;GQ=99;MLEAC=2;MLEAF=1;MQ=70;QD=33.77;SOR=0.907;TCov=89045 GT:AD:DP:GQ:PL:AF 1/1:0,503:503:99:17016,1519,0:0.8390000000000001

Program ends with Segmentation fault: 11 and no output is produced. Log file is empty

[Hyun Min Kang]

You need to provide population-allele frequency, not a single-individual allele frequency.

Hyun.

-----------------------------------------------------
Hyun Min Kang, Ph.D.
Associate Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu

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[Swati Goyal]

Hi Hyun,

It was population frequency from gnomad denoted by AF in format field. 

There was a new line character at end of line that threw "segmentation" error. Removing that runs the program fine.

I have some more questions if you could help -

1. Is there a minimum number of SNV recommended to run this tool successfully ? i have ~40 SNV per sample

2. Assuming that i need more than 40 in single file. Should i crate multi sample vcf, and multi sample bam file ?

3. Does it matter if AF is added to INFO or Format feild ?

Thanks.

[Hyun Min Kang]

You need AF in the INFO field. The paper recommend at least 1,000 SNPs. Individual genotypes do not matter unless you use --chip-mix option. It is unclear why you get segfault. Please share the full command line and BAM headers too.

Hyun.

-----------------------------------------------------
Hyun Min Kang, Ph.D.
Associate Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu

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